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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccaggcagttatcccagtccacgaagcaagcaggccctatattagatatttgttgtttaactcattttgcctgtttgtttctgatttattttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTCGAACATATCCCAGAGTTGGTTGCTACTTCTACTGA

Basic information

species Zea mays
transcript GRMZM2G423027_T05
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423027_T05 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g44280.2 (Oryza sativa), 3'ss of exon 2
tgccaggcagttatcccagtccacgaagcaagcaggccctatattag-atatttgttgtttaactcattttgcctgttt--gtttctgatttattttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTCGAACATATCCCAGAGTTGGTTGCTACTTCTACTGA
 |      | ||  || ||   |       | |||     | |||   |||  ||||  | |||||   |||| | |||  || |||    ||  ||   ||||||| || |||||||| |||||||| ||  | |||||||||||||||||||||||||||||||| ||||||||||||||||||||| || | |||| |||
-gtttaatattt--cctagctgaaatgctcaacagatagcaaatttctatacatgtttgtcaactcgcattgcttatttacgtatctttgataacttcaacagGCACAGGGTACCTAACAGCTTGCTTCGCGATTATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTTGAACATATCCCAGAGTTGGTTACTTCGTCTATTGA

upper sequence: GRMZM2G423027_T05 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G02810.1 (Glycine max), 3'ss of exon 2
tgccaggcagttatcccagtccacgaagcaagcaggccctatattagatatttgttgtttaact-cattttgcctgtt-tgtttctgattta---ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTCGAACATATCCCAGAGTTGGTTGCTACTTCTACTGA
      ||   |||     |  |    |   | |    | ||      | | | |   ||  || |||||         ||||  |  |||       |||||||| || |||||||| || || ||||||||  |||||||||||||  |||| || ||  |||| || |||||||| || ||||||||| ||  ||| |  ||
-----tgctactatatagatttaactggagtggaatttcaatgcattttttctctgaattctctgcatttgatgcacaatgttcatactttggacccctttgcagGAACGGGATACCTGACAGCATGCTTTGCCTTGATGGTTGGACCCCAAGGCCGTGCTATTGGCGTGGAACATATTCCTGAGTTGGTTTCTTTTTCAATCGA

upper sequence: GRMZM2G423027_T05 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G13480.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------------tgccaggcagttatcccagtc---cacgaagcaagcaggccctatatt---agatatttgttgtttaactcattttgcctgtt------tgtttctgattta---ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTCGAACATATCCCAGAGTTGGTTGCTACTTCTACTGA
                                                                             |||      ||| | |    |   |||  |   | ||||      | |   |   |||| |   |  | ||  ||    || |      | ||  |  |||       ||| |||| || |||||||| ||||| ||||||||  ||||||||||||| ||||| || ||  ||||||| |||||||| || || |||| | ||  ||| | |||
gtgtgaagattttataatgtaaaaccttgactgtgacaattagttttctctcatagatttgcataatcccaattcaatgcggaaacgttgtacgtaccacacacagatttaacaggaatggaactttaatgcatttttctctgcattctcttcatttgatgcgcaatattcatattttggacccctttacagGAACGGGATACCTGACTGCATGCTTTGCCTTGATGGTTGGACCCGAAGGCCGTGCTATTGGTGTGGAACATATTCCTGAATTGGGTTCTTTTTCAATTGA

upper sequence: GRMZM2G423027_T05 (Zea mays), 3'ss of exon 3
lower sequence: AT3G48330.1 (Arabidopsis thaliana), 3'ss of exon 2
tgccaggcagttatcccagtccacgaagcaagcaggccctatattagatatttgttgtttaactcattttgcctgtttgtttctgatttattttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTCGAACATATCCCAGAGTTGGTTGCTACTTCTACTGA
                  ||        |   |    | |  |||||   |||  |   |   || | ||||   ||||  | ||||  |||||    ||| || || ||| ||||||||||||||||  | ||||||||| | |||||||| ||  ||||||| |||||||| || || ||||| ||| |||||  | |
------------------gtttgttttactttctcttcttgaattag---ttttgtacattcttcttcttgct--tttgaatatgatgaattttg-atagGGACCGGGTACTTAACTGCTTGCTTTGCGGTTATGGTTGGAACCGAAGGGCGTGCTATTGGTGTGGAACATATTCCTGAATTGGTGGCTTCTTCTGTTAA

upper sequence: GRMZM2G423027_T05 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g09690.t01 (Vitis vinifera), 3'ss of exon 2
tgccaggcagttatcccagtccac-gaagcaagcaggccctatattagatatttgttgtttaactcattttgcctgtttgtttctgatttattttt----tgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTCGAACATATCCCAGAGTTGGTTGCTACTTCTACTGA
       |||  || | | ||| | | ||      |   ||  |||   |  |  ||    |    || || ||||    ||| |  ||| |||||    |  ||| || || ||  | || || |||||||||||||||||||||||| ||||  | |||||||| || ||||| || || |||||||||||| |||| |   |
-----tacagaaatgcaaatcctctgcagtttctggattctgcatttctttgtgattaaagattctatattacctgaccattttttttttttttttaaattttagGAACGGGGTATTTGACAGCCTGCTTTGCACTGATGGTTGGACCACAAGGTTGTGCAGTTGGAGTAGAACACATACCTGAGTTGGTTGCTTCTTCAATCAA

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|211178416|gb|FL087632.1|FL087632
EST:     ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAG                         GCACTGGATAC
genomic: ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAGgtaacttatt ... ttttttgcagGCACTGGATAC
EST: gi|211178414|gb|FL087630.1|FL087630
EST:     ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAG                         GCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGGACCAGAAGGG
genomic: ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAGgtaacttatt ... ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGG-ACCAGAAGGG
EST: gi|101382804|gb|EB813457.1|EB813457
EST:     ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGG-CA-                         -C--TGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
genomic: ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAGgtaacttatt ... ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
EST: gi|211178420|gb|FL087636.1|FL087636
EST:     ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAG                         GCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
genomic: ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAGgtaacttatt ... ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
EST: gi|71446834|gb|DR827884.1|DR827884
EST:     ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAG                         GCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
genomic: ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAGgtaacttatt ... ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
EST: gi|71442718|gb|DR823768.1|DR823768
EST:     ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAG                         GCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
genomic: ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAGgtaacttatt ... ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
EST: gi|211178419|gb|FL087635.1|FL087635
EST:     ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAG                         GCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
genomic: ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAGgtaacttatt ... ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
EST: gi|211322149|gb|FL087639.1|FL087639
EST:     ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAG                         GCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTG
genomic: ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAGgtaacttatt ... ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTG
EST: gi|71442719|gb|DR823769.1|DR823769
EST:     ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAG                         GCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC
genomic: ACTGGAGAAGAATCTTCAGCCTGGAATGCGAGCTCTCGATGTTGGGTCAGgtaacttatt ... ttttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatatttgttgtttaactcattttgcctgtttgtttctgatttattttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTCGAACATATCCCAGAGTTGGTTGCTACTTCTACTGA
                                   ttctgat  putative branch site (score: 3)
                                         tttatttttt  CT-rich tract
                              tttgtttctgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccaggcagttatcccagtccacgaagcaagcaggccctatattagatatttgttgtttaactcattttgcctgtttgtttctgatttattttttgcagGCACTGGATACCTAACTGCTTGCTTTGCACTGATGGTTGGACCAGAAGGGCGAGCAGTTGGTGTCGAACATATCCCAGAGTTGGTTGCTACTTCTACTGA

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