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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgttcatttcttcctgcacaataggcttgtttaggttctctagttttctggtgtgtagatctctttcaccttatgatgtctttctgtttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCATCGCAG

Basic information

species Glycine max
transcript GLYMA13G19950.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 4
ctttgttcatttctt--cctgcacaataggcttgtttaggttctctagttttctggtgtgtagatctctttcaccttatgatgtctttctgtttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCATCGCAG
 | ||| |||   ||   |||  | |     |  || |   | |     | |        | | |  || |       | |||   |  | |||  |  ||||||||||||||||||||||| ||||| ||||| ||||   |||| || || |||||||| ||||||||||| ||||| || || |||
ttatgtgcatactttagtctgtgcgagcaaatctttgaatatatgggaatctgacaacaattgctaactgtgggtcctttatgctgtaatattttca--cagCATAAAACTATTGATAGTGTCCTGGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGTTCTGATCTAAGTGCTGCTTCTCAG

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 5
ctttgttcatttcttcctgcacaataggcttgt-ttaggttctctagttttctggtgt--gtagatctctttcaccttatgatgtctttctgtttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCATCGCAG
 | ||| |||   ||  | | |  |  ||   | || |  | | | |   ||||      |    |   | |   |   | |||  ||  | |||   ||||||||||||||||||| ||||| || || ||||| ||||   |||| || || |||||||| || |||||||||||||| || || |||
ttatgtgcatactttagt-ctctgtgcgcaaatctttgaatatatgggaatctgaccacagctactaattgtgggccctttatgatttaatatttt--aacagCATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G58180.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------ctttgttcatttcttcctgcacaataggc-ttgtttaggttctctagttttctggtgtgtagatctctt--------tcaccttatgatgtctttctgtttataa-acagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCATCGCAG
                                       ||||| |   || || |    |||||        ||   | |  ||  ||  || |    || || |||        ||   ||||| || ||||   ||||||  |||||||||||| |||||| |||| || ||  |||| || ||||||||||| ||||| |||||||| || ||  | ||    |||||| ||
gtaagtgccgtccctggttcttgattgttgacctgcatgctttgcttcctttttacattccaatacataccagttccctccattaagttcttgtttccaaggtcgcttaaacatggtcgttttatgctgacttttgttttatactacagCATAAAACCATTGATGGTGTCCTAGCCCGAGGTGAAAAGCTGGACAGCTTAGTGGAGAAGAGCTCAGAGTTAAGCCTGGCATCGAAG

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 4
ctttgttcatttcttcctgcacaatag-gcttgtttaggttctctagttttctggtgtgtagatctctttcaccttatgatgtctttctgtttataa-acagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCATCGCAG
  | |   | |   | |||   |||   | ||  ||   | ||    |||  |  | | |   | |  ||  | ||   |||| ||| | | | | | ||||||||| |||||||||||||| || ||  |||| |||||||||||||||||||||||||| ||||| ||||| ||  | ||||| |||
--tggagaactatctgctgtctaattttgtttccttttttccttctttttatttttctatctttattcttttctttgatatgtatttttctgtttgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG

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|298168422|gb|HO009352.1|HO009352
EST:     ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCT
genomic: ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgc ... ttataaacagCATAAAACTATTGATAGTGTGCT
EST: gi|192306907|gb|FK002629.1|FK002629
EST:     ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT                         CATAAAACTATTGATAGTGTGTTGGCTAGAGGGGAGAAGCTGGACAGCTTA
genomic: ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgc ... ttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
EST: gi|192299559|gb|FG987720.1|FG987720
EST:     ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
genomic: ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgc ... ttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
EST: gi|151393215|gb|EV263090.1|EV263090
EST:     ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
genomic: ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgc ... ttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
EST: gi|192306908|gb|FK002630.1|FK002630
EST:     ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT                         CATAAAACTATTGATAGTGTGTTGGCTAGAGGGGAGAAGCTGGACAGCTTA
genomic: ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgc ... ttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
EST: gi|151407036|gb|EV275591.1|EV275591
EST:     ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
genomic: ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgc ... ttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
EST: gi|298197444|gb|HO044923.1|HO044923
EST:     ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
genomic: ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgc ... ttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
EST: gi|213611777|gb|DB964781.1|DB964781
EST:     ACAAGTTGATGNAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
genomic: ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgc ... ttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
EST: gi|192294833|gb|FG987522.1|FG987522
EST:     ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
genomic: ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgc ... ttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
EST: gi|208126796|gb|GD926054.1|GD926054
EST:     ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
genomic: ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgc ... ttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
EST: gi|213602294|gb|DB958554.1|DB958554
EST:     ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTT                         CATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA
genomic: ACAAGTTGATGAAAATTCAGAGAGAGTTGGATGAAACAAAAATCATCCTTgtaagcatgc ... ttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttctggtgtgtagatctctttcaccttatgatgtctttctgtttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCATCGCAG
                                    tctttctgttt  CT-rich tract
                                      tttctgtttataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgttcatttcttcctgcacaataggcttgtttaggttctctagttttctggtgtgtagatctctttcaccttatgatgtctttctgtttataaacagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCATCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - tcctgca
- - - - - - - - - - - - - -gcttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttctg