Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgtcgtggacataaaattttgcatttttttcttcttttcagctgttcaatatatcagtcctattcttgacgtgttatgatctttctacttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG

Basic information

species Zea mays
transcript GRMZM2G090904_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g21970.1 (Oryza sativa), 3'ss of exon 2
----cctgtcgtggacataaaattttgcatttttttcttcttttcagctgttcaatatatcagtcctattcttgacgtgttatgatctttctacttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG
      |||  ||||  |  |   || | ||| |   || | |   | | ||    |||  ||| || ||||||| |   |      ||| | | | | | ||||| ||||| ||||| || || || ||||||||||| || |||||||||||||| ||||| ||||| |||||||||||||||||||| |||||||||||||
gctttatgttttggatgttgagactt-cgtttgtagattttctatggtttttgggcatactagttcttttcttgatgaagttc---ttttattcatttgtttagGGACCTAGGATGGTTCGAGATGTATTCCGTTTGGCTAAAGAGAATGCCCCAGCTATCATATTCATCGATGAGGTTGATGCTATAGCAACTGCTCGTTTTG

upper sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 2
-cctgtcgtggacataaaattttgcatttttttcttcttttcagct-gttcaatatatcagtcctat-tcttgacgtgttatgatctttctacttct-ttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG
 |||   ||   |    | |||   ||   ||  || | |     | | |||||   | ||  | |  |||| |  | ||     | | | | || | || ||||| ||  ||||||| ||||| || || ||| | || || |||||||| || || || || || ||||||||||||||||| |||||||||||| | ||||
tcctaaagtttcctaggagtttcaaatccattgattgtatgtgttttgatcaatggtttagagcaacatcttcaaatctt----ccctgccatttttattttagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCTATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTTG

upper sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G05730.1 (Glycine max), 3'ss of exon 2
--cctgtcgtggacataaaattttgcatttttttcttcttttcagctgt-tcaatatatcagtcctat-tcttgacgtgttatgatctttctacttct-ttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG
  |||   ||   |      |||   |||  ||  || | |       | |||||   | ||  | |  |||| |  | ||     | | | | || | ||  |||| ||  ||||||| ||||| || || ||| | || || ||||||||||| ||||| || || ||||||||||||||||| |||||||||||| | ||| 
ctcctaaagtttcctgggggtttcaaattcattgattgtatatgttcttatcaatggtttagagcaacatcttcaaatctt----ccctgccatttatatttcaGGGTCCACGAATGGTCCGTGATGTATTTCGTCTTGCTAAAGAGAATGCCCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACTGCTAGATTT-

upper sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G31450.1 (Glycine max), 3'ss of exon 2
-cctgtcgtggacataaaattttgcatttttttcttcttttcagct-gttcaatatatcagtcctat-tcttgacgtgttatgatctttctacttct-ttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG
 |||    |        | |||   |||  ||  || | |     |   |||||   | ||  | |  |||| |  | ||     | | | | || | ||  |||| ||  ||||||| ||||| || || ||| | || || |||||||| || ||||| || || ||||||||||||||||| |||||||| ||| | ||||
tcctaaaatttcttgggagtttcatattcgttgattgtatatgttttaatcaatggtttagagcaacatcttcaaatctt----ccctgccatttatatttcagGGTCCACGAATGGTTCGTGATGTATTTCGTCTCGCTAAAGAGAATGCGCCTGCAATTATATTTATTGATGAGGTTGATGCAATAGCCACGGCTAGATTTG

upper sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G58290.1 (Arabidopsis thaliana), 3'ss of exon 2
cctgtcgtggacataaaattttgcatttttttcttcttttcagctgttcaatatatcagtcctattcttgacgtgttatgatctttctacttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG
            || |||  |   |  ||| |      || ||  || | ||  | |  | |||||  ||  |  | |     ||| ||     ||| |||| ||| | ||||| ||||| || |||||| | |||||||| ||||| ||||| ||||| |||||||||||||| ||||| || || |||||| | ||||
----------gtattaaaaatcatagctttattgaaggtttag--gtcctattgagcgattctatt--tggtgactaactggtttttta----attgcagGGACCTCGTATGGTTCGTGATGTCTTCCGTCTTGCCAAGGAAAATGCTCCAGCTATCATCTTCATTGATGAGGTAGATGCCATCGCTACTGCTAGGTTTG

upper sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 2
cctgtcgtggacataaaattttgcatttttttcttcttttcagc--tgtt-caatatatc--agtcctattcttgacgtgt-tatgatctttctacttctttgt--agGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG
         |   | || | ||  || ||||     ||  ||    || | |||||      | |  || | |     | | |||  | ||| |   |  || |  |||| || |||||||| ||||| || |||||| | |||||||||||||| || ||||| || ||||||||||||||||||||||| || || ||| | ||||
--------tggttttaattgttttatcttttctagattgccaatattgctgcaatacccttaaattttaatttatctatatatatattttttttctcttgttatcaagGGTCCGAGAATGGTCCGTGATGTTTTCCGTCTTGCCAAGGAGAATGCTCCTGCAATTATCTTCATTGATGAGGTTGATGCTATTGCTACCGCTAGGTTTG

upper sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S79_171V6.1 (Physcomitrella patens), 3'ss of exon 2
cctgtcgtggacataaaattttgcattttt---ttcttcttttcagctgttcaatatatcagtcctattcttgacgtgttatgatctttctacttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG
 |  |  |   ||  | || |||   ||     ||| | |||     ||   | | |      | |  | || |  |   | ||  | |  | ||  |  ||||| ||  | ||||| |||||||| |||||  |||| ||||||||||||||||| || || |||||||||||| ||||||| || || || ||||||||||
-caattcttt-caggagatcttgttgttcagcgttcatgtttctgaatgccaattgtgctgtgcttgatattaaaataa-acgaaatgtaaattttgtcatagGGTCCCCGCATGGTACGTGACGTATTCCGACTGGCAAAGGAGAATGCCCCAGCCATTATCTTCATTGATGAGATTGATGCAATTGCGACAGCTCGTTTTG

upper sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S243_67V6.1 (Physcomitrella patens), 3'ss of exon 2
cctgtcgtggacataaaattttgcatttttttcttcttttcagctgttcaatatatcagtcctattcttgacgtgttatgatctttctacttctttgt------agGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG
       |  |   ||  ||||      || || |  |   ||||  |   ||| |     | |       |||||||  |  | | || |    |||      |||| ||  | ||||||||||| ||||||||  |||| |||||||| |||||||| || || || ||||||||  ||||||| || || || |||||||| |
-----actttattaaatgttttctggaattatcgtagtcatagcttgtttttat-tagacgccagctaacccgtgttagaaaatatgtaatgtaatgtggtctcagGGTCCCCGTATGGTGCGTGATGTGTTCCGACTGGCGAAGGAGAACGCCCCAGCCATTATCTTTATTGATGAAATTGATGCAATTGCAACAGCTCGTTTCG

upper sequence: GRMZM2G090904_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S36_183V6.1 (Physcomitrella patens), 3'ss of exon 2
cctgtcgtggacataaaattttgcatttttttcttcttttcagctgttcaatata-tcagtcctattcttgacgtgttatgatct----ttctacttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG
    |  ||     || ||  | | ||  |||||  |  |||    ||  | |   || | | |||| |   | |    ||| ||    |    | |  ||  |||| ||  | ||||||||||| || |||||| | || ||||||||||||||||| || || || ||||||||| ||||||| || || || ||||||||||
----ttatgt-tgcaagataatcctttcgtttctggtaatcaatcattttaaaccctcgggcttattttcagcttcacttgaactcatgtgtagccttattacagGGTCCCCGTATGGTGCGTGATGTATTCCGTCTAGCGAAGGAGAATGCCCCAGCCATTATATTTATTGATGAGATTGATGCAATTGCAACAGCTCGTTTTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|31997670|gb|CD661707.1|CD661707
EST:     TCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: TCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|50333575|gb|CO528701.1|CO528701
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGGGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGG
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGG
EST: gi|19437228|gb|BM953638.1|BM953638
EST:     CTTTTATCAGGGTCGNCGGTTCAGAGCTTGCTCAAAAGCACTTGGGTGAG                         GGCCCTAGAATGGTGCGT
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGT
EST: gi|22819685|gb|BU499775.1|BU499775
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|116813718|gb|EC856200.1|EC856200
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|21760243|gb|BQ635784.1|BQ635784
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|211390318|gb|FL404124.1|FL404124
EST:     TTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: TTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|32937253|gb|CF042072.1|CF042072
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTCCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|149077094|gb|EE165751.2|EE165751
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGA
EST: gi|60672392|gb|DN475143.1|DN475143
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACCTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|31364533|gb|CD448888.1|CD448888
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|60400635|gb|DN233442.1|DN233442
EST:     AGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: AGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|60342267|gb|DN209240.1|DN209240
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|148931425|gb|EC874380.2|EC874380
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTG-CCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|149106686|gb|EE188582.2|EE188582
EST:     CAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|60400510|gb|DN233317.1|DN233317
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|71448676|gb|DR829726.1|DR829726
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGTCAANGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|5915467|gb|AW053108.1|AW053108
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|31910991|gb|CD651701.1|CD651701
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|149044685|gb|EE047658.2|EE047658
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|6095497|gb|AW120164.1|AW120164
EST:     CAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|113856905|gb|DW980636.1|DW980636
EST:     TTTATCAGGGTCGTCGGTTCAAAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCC
genomic: TTTATCAGGGTCGTCGGTTC--AGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCC
EST: gi|148937643|gb|EC881836.2|EC881836
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|71762983|gb|DR960920.1|DR960920
EST:     GTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: GTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|110516945|gb|EE021532.1|EE021532
EST:     GGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTGGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: GGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|60357801|gb|DN224774.1|DN224774
EST:     AGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: AGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|22819703|gb|BU499793.1|BU499793
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|22819070|gb|BU499160.1|BU499160
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|211254934|gb|FL426618.1|FL426618
EST:     TTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: TTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|5296120|gb|AI782995.1|AI782995
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|31362941|gb|CD447298.1|CD447298
EST:     CAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|60356494|gb|DN223467.1|DN223467
EST:     TTCAGAGTTTGTTCAAAAGTACTGGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: TTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|113702567|gb|EE680071.1|EE680071
EST:     CGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGGTTGGCCAAGGAGAATGCCCCA
genomic: CGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|6022605|gb|AW067417.1|AW067417
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|148970781|gb|EE021533.2|EE021533
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
EST: gi|116817277|gb|EC860100.1|EC860100
EST:     CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAG                         GGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA
genomic: CTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 390

TACTGGCAAGACCATGCTTGCCAAAGCAGTTGCACATCATACCACTGCTGCTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 424

TACTGGCAAGACCATGCTTGCCAAAGCAGTTGCACATCATACCACTGCTGCTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 390

TACTGGCAAGACCATGCTTGCCAAAGCAGTTGCACATCATACCACTGCTGCTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 347

TACTGGCAAGACCATGCTTGCCAAAGCAGTTGCACATCATACCACTGCTGCTTTTATCAGGGTCGTCGGTTCAGAGTTTGTTCAAAAGTACTTGGGTGAGgtaagttggg ... ttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcaatatatcagtcctattcttgacgtgttatgatctttctacttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG
                    tcttgac  putative branch site (score: 347)
                                    tctttctacttctttg  putative PPT
     atatatca  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgtcgtggacataaaattttgcatttttttcttcttttcagctgttcaatatatcagtcctattcttgacgtgttatgatctttctacttctttgtagGGCCCTAGAATGGTGCGTGACGTGTTCCGTTTGGCCAAGGAGAATGCCCCAGCAATCATTTTCATTGATGAGGTTGATGCTATAGCCACTGCTCGTTTTG

- - - - - acataaa
- - - - - - - - - - ttgcatt
- - - - - - - - - - - - - - - - - - - -tcagctg