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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttcacaactgctgggatgttgtgattttcagcaccaatcctttgtcgtcactagtcaaatcctaactaatcatgccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGCCCGGGTGGCTGGAAAGTGCTCGTTGAATACTATGACAGCTTGGTGCCAT

Basic information

species Zea mays
transcript GRMZM2G051270_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051270_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g53230.1 (Oryza sativa), 3'ss of exon 4
gtaagtt----ttcacaactgc--tgggatgttg--tgattttcagcaccaatcctttgtcgtcactagtcaaatcctaacta-atca--tgccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGCCCGGGTGGCTGGAAAGTGCTCGTTGAATACTATGACAGCTTGGTGCCAT
||||  |    ||||   |||   ||| |       | ||||| |||||||||  ||| |     | || | | ||||||| | ||    ||  ||||  ||||||| ||||||||||||||| || |||| ||||| || || || |||||||||||||||||||| || || ||||||||||| |||||||||  |||||
gtaacatccatttcaatcctgttttggtacaccagttaattttgagcaccaatgttttttt----ccagcccagtcctaacaacattgcctgtgttatatagATGCGTACTCTTGCCAAGAACTGCCAGAGCCCCCCTGACGGATTCATGTGCCCGGGTGGCTGGAAGGTCCTTGTTGAATACTACGACAGCTTGACGCCAT

upper sequence: GRMZM2G051270_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G38760.1 (Glycine max), 3'ss of exon 4
-gtaagttttcacaactgctgggatgttgtgattttcagcaccaatc-ctttgtcgtcactagtcaa----atcctaactaatcatgcct---tattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGCCCGGGTGGCTGGAAAGTGCTCGTTGAATACTATGACAGCTTGGTGCCAT
    | |||  | |  |      ||| |||   ||     |  | |  || |||  | ||   ||      ||  |||| ||   | | |   | | ||||||||||| || || | ||||   || ||||| || ||||| ||||||||||| ||||| ||||| ||||| ||||| |||||||| ||||| || |  |
aagtactttctagacgtcacaaaatggtgttcattgtgataatagtgactatgttcttacatatctgtagtatgttaacaaaggttacttgcatttacagATGCGCACACTGGCAAGGAACAAAGAAAGTCCTCCTGATGGATTTATGTGCCCTGGTGGATGGAAGGTGCTGGTTGATTACTATGATAGCTTAGTACTCT

upper sequence: GRMZM2G051270_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G28980.2 (Glycine max), 3'ss of exon 4
------gtaagtttt-cacaactgctgggatgttgtgattttcagcaccaatcctttgtcgt-cactagtcaaatcctaactaat----catgccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGCCCGGGTGGCTGGAAAGTGCTCGTTGAATACTATGACAGCTTGGTGCCAT
       || || |  || ||  |   |    || ||||  | ||    | |   || |     | | ||   ||  |||| ||     | ||| || | ||||||||||| || || | ||||   || || || || ||||| ||||||||||| ||||| ||||| || || |||||||||||||| ||||| || |  |
tattttctaggtgtaacataatggt--gttcattatgataat-agtgtgagtatgttattacatatttgtagtatgttaacaaaggttacttgcattttacagATGCGCACACTGGCAAGGAACAAAGAAAGCCCTCCTGATGGATTTATGTGCCCTGGTGGTTGGAAGGTACTGGTTGAATACTATGATAGCTTAGTACTCT

upper sequence: GRMZM2G051270_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT3G22890.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagttttcacaactgctgggatgttgtgattttcagcaccaatcctttgtcgtcactagtcaaatc-ctaactaatcatgccttattc-agATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGCCCGGGTGGCTGGAAAGTGCTCGTTGAATACTATGACAGCTTGGTGCCAT
||||   |  || | | ||    ||||   ||| |    |       |||||  | |  |  |||| | |||| |  |  |   |||||| ||||||||||  | || ||||||  ||| |  || || || |||||||||||||| ||||| |||||||| || || || |||||||| ||||||   ||  
gtaa---tataccagtcctacattgttaaaattcttcatag------tttgt--ttataaaacaaacctctaaatgtttttcgattattctagATGCGCACATTGGCAAAGAACAACGAAAACCCGCCAGACGGTTTTATGTGCCCAGGTGGATGGAAAGTTCTGGTGGATTACTATGAGAGCTTGACTCCGG

upper sequence: GRMZM2G051270_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv05s0020g04210.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------------------------gtaagttttcacaactgctgggatgttgtgattttcagcacc--aatcctttgtcgtcactagtcaaatcctaactaatcatgccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGCCCGGGTGGCTGGAAAGTGCTCGTTGAATACTATGACAGCTTGGTGCCAT
                                                                          | || || |    ||||  || |||   |  |||||| ||    |||  ||  | |    |  |      | |       |    ||   |||||| | ||||| || ||||||   ||||  || || || || ||||||||||||||||| ||| ||||| | || ||||| |||||||| ||||||||  
gtatattttttgcataggaaaaaaatgcagacctctttttttatttcatatctaatgataatcccaaaatggctgaaaattattcagactg--ggcatgc-atttttttcaacatggaaatatttgatggatgatgtttctgaacaaggccgctacattttg--cagATGAGAACTCTAGCGAAGAACAAAGAGAACCCTCCAGACGGATTTATGTGCCCGGGTGGTTGGGAAGTGTTGGTGGAATATTATGACAGTTTGGTGCCCA

upper sequence: GRMZM2G051270_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ22935 (Selaginella moellendorffii), 3'ss of exon 4
gtaagttttcacaactgctgggatgttgtgattttcagcaccaatcctttgtcgtcactagtcaaatcctaactaatcatgccttatt-cagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGCCCGGGTGGCTGGAAAGTGCTCGTTGAATACTATGACAGCTTGGTGCCAT--
                                |||  || |   |  ||   | ||  |  | ||||  |||| |    |     | | |||||| | |   ||||||||| | |||| ||||| || || || || |||||||| || ||||||||||| ||||||||||||||  | |||     ||||   
-------------------------------gtttgtgctctttttattctgcatcctt--ttaaat--taacgagctttctggaaatgcagATGAGAAACTTTGCCAAGAGCGGCGAAAGTCCACCAGACGGGTTCATGTGCCCCGGGGGCTGGAAAGTCCTCGTTGAATACTACCAAAGC--AAAGCCAAGG

upper sequence: GRMZM2G051270_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ32830 (Selaginella moellendorffii), 3'ss of exon 4
gtaagttttcacaactgctgggatgttgtgattttcagcaccaatcctttgtcgtcactagtcaaatcctaactaatcatgccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGCCCGGGTGGCTGGAAAGTGCTCGTTGAATACTATGACAGCTTGGTGCCAT--
                         ||||| | ||        || ||   ||||    | | ||     | ||           || |||||| | |   |||||||||   |||| ||||| || || || || |||||||| || ||||||||||| ||||||||||||||  | |||     ||||   
-----------------------gtttgtgctcttt-----ttattctccatcgttttaaattaagg---agctgtctggaa---atgcagATGAGAAACTTTGCCAAGAGTGGCGAAAGTCCACCAGACGGGTTCATGTGCCCCGGGGGCTGGAAAGTCCTCGTTGAATACTACCAAAGC--AAAGCCAAGG

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|32840519|gb|CD980200.1|CD980200
EST:     TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATG
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATG
EST: gi|32836595|gb|CD976273.1|CD976273
EST:     TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCNCCGGATGGTTNTATG
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATG
EST: gi|111191745|gb|EE289881.1|EE289881
EST:     TTTTCGATCCATCAAGGAAAGATGATTTCTTTTTCATTTTTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
EST: gi|110219906|gb|EC901804.1|EC901804
EST:     TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
EST: gi|12046747|gb|BF728886.1|BF728886
EST:     TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAAC
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAAC
EST: gi|110961857|gb|EE181909.1|EE181909
EST:     TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
EST: gi|148943164|gb|EC888223.2|EC888223
EST:     TTTTCGATCCATCAAGGAAAGATGATTTCTTTTTCATTTTTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
EST: gi|149102605|gb|EE287963.2|EE287963
EST:     TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATTTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
EST: gi|149076868|gb|EE165524.2|EE165524
EST:     TTTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATTTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
EST: gi|76921061|gb|DV168441.1|DV168441
EST:     TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
EST: gi|32926464|gb|CF031276.1|CF031276
EST:     TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
EST: gi|32924998|gb|CF029810.1|CF029810
EST:     TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
EST: gi|32842063|gb|CD981744.1|CD981744
EST:     TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATG
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATG
EST: gi|110533959|gb|EE038139.1|EE038139
EST:     TTTTCGATCCATCAAGGAAAGATGATTTCCTTTTCATTTCTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
EST: gi|111190608|gb|EE288744.1|EE288744
EST:     TTTTCGATCCATCAAGGAAAGATGATTTCCTTTTCATTTTTGGCACAAAG                         ATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC
genomic: TCTTCGATCCATCAAGGAAAGATGATTTCCTCTTCATCTCTGGCACAAAGgtaagttttc ... ccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcaccaatcctttgtcgtcactagtcaaatcctaactaatcatgccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGCCCGGGTGGCTGGAAAGTGCTCGTTGAATACTATGACAGCTTGGTGCCAT
                                             ccttattc  CT-rich tract
                                 taactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttttcacaactgctgggatgttgtgattttcagcaccaatcctttgtcgtcactagtcaaatcctaactaatcatgccttattcagATGCGCACTCTTGCCAAGAACCGCGAGAGTCCCCCGGATGGTTTTATGTGCCCGGGTGGCTGGAAAGTGCTCGTTGAATACTATGACAGCTTGGTGCCAT

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