Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatggttgaatgcatttcttttacttttttaaaatcacaatggttaattcaatatgttgtttaatttttttggggggtatttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCTAAGCAGAAGAAAAAGAAGGGTAAAGCACAAAAGGCCTGTTCGATATTGT

Basic information

species Glycine max
transcript GLYMA01G36880.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacatggttgaatg-catttcttttacttttttaaaatcacaatggttaattcaatatgttgtttaatttttttggggggtatttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCTAAGCAGAAGAAAAAGAAGGGTAAAGCACAAAAGGCCTGTTCGATATTGT
||| | |  | || | ||| || |  |   | ||       |  || |  ||||   || || || |          | |    | | |||||||||||||||  || ||||||||||| || ||||| ||||||||||| || ||||||||||||||||||   ||||||||||||||||| || || ||||
gtaaacgaataaaagacatctcatgaatcatctt-----ttcggtgttggattcttcatctt-ttgatgaaaacaatgtgactataactgcagAACGTGAAGGGCGTGTTTGATGCAGCGATCAGAGTGGTCCTTCAACCTCCAAAGCAGAAGAAAAAGAAGAACAAAGCACAAAAGGCCTGCTCCATCTTGT

upper sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------------------------------------gtacatggttgaatgcatttcttttacttttttaaaatcacaatggttaattcaatatgttgtttaatttttttggggggtatttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCTAAGCAGAAGAAAAAGAAGGGTAAAGCACAAAAGGCCTGTTCGATATTGT---
                                                                 |  |  | |     |    |||| |||| ||    |     |  | ||   |   |    || ||    |||| ||  |  | |||||||||  | |||||||| ||||||   ||||| || ||||| || |||||||| ||||||||||||||||||   ||||   |  ||| ||| || |||||||   
gtttatattctattaacaatttttgtacttcatgtatattgtctgatttctttcacatacaataaatgtaatagttcttagagttttttctttcttttttttttttttttaaaaaaagggttcgattgaagcactttgtggacttgtaattgcagAATATCAAGGCAGTGTTTGATCAGGCCATTAGGGTTGTGCTCCAACCACCCAAGCAGAAGAAAAAGAAGT-CAAAGTCTA--AGGTCTGCTCCATATTGTGAA

upper sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 7
gtacatggttgaatgcatttcttttacttttttaaaatcacaatggttaat-tcaatatgttgtttaatttttttggggggta-------tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCTAAGCAGAAGAAAAAGAAGGGTAAAGCACAAAAGGCCTGTTCGATATTGT--
|  ||           |  |||   | || |  |  ||  |  |  ||    |  | |           | || ||  | ||        || ||||||||| ||||| ||||| ||||||||||| || |  || || ||||| ||||| ||||||||||| |||||    |||  |||||||  ||||   ||| | |  
ggtcacaacgtgtcatagctctagcaattgtagatgattccggtaattggcgtttaaacaacaccgccatcttctgatgcgttgctgtctttcattgcagAATGTGAAAGCAGTTTTTGATGCAGCAATCAAGGTGGTTCTTCAGCCACCCAAGCAGAAGAAGAAGAAA---AAAAAACAAAAGAACTGTGTCATACTCTGA

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|6746963|gb|AW317419.1|AW317419
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|9819855|gb|BE555431.1|BE555431
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|26268044|gb|CA819107.1|CA819107
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|26057126|gb|CA800040.1|CA800040
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|5057669|gb|AI736145.1|AI736145
EST:     GCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: GCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|193380083|gb|FK348265.1|FK348265
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTC-AAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|31455813|gb|CD397841.1|CD397841
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|38193058|gb|CF922264.1|CF922264
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|5175630|gb|AI759963.1|AI759963
EST:     TGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAGAGACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGTCATAAGAGTTGTNCTTCAACCA
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCA
EST: gi|31306633|gb|CD391836.1|CD391836
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|7925509|gb|AW831535.1|AW831535
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTCGTTCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|31469737|gb|CD411765.1|CD411765
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|17519189|gb|BM188231.1|BM188231
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|21600999|gb|BQ611321.1|BQ611321
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|14991554|gb|BI317227.1|BI317227
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|31309981|gb|CD395184.1|CD395184
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
EST: gi|31458682|gb|CD400710.1|CD400710
EST:     AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAG                         AACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT
genomic: AGCTGATTAATGCGCCAGCTTACATTGAATGCAGTTCAAAAACACAGGAGgtacatggtt ... tttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacaatggttaattcaatatgttgtttaatttttttggggggtatttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCTAAGCAGAAGAAAAAGAAGGGTAAAGCACAAAAGGCCTGTTCGATATTGT
                        gtttaat  putative branch site (score: 4)
         ttaattcaatatgttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatggttgaatgcatttcttttacttttttaaaatcacaatggttaattcaatatgttgtttaatttttttggggggtatttattgcagAACGTGAAGGCAGTCTTTGATGCAGCCATAAGAGTTGTCCTTCAACCACCTAAGCAGAAGAAAAAGAAGGGTAAAGCACAAAAGGCCTGTTCGATATTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG