Sequence
atgc intronic sequence ATGC exonic sequence...atgagtggagttgcactttaatgtatatgatataggcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
Basic information
species | Glycine max |
transcript | GLYMA13G25570.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02270.t01 (Vitis vinifera), 3'ss of exon 4
atgagtggagttgcactttaatgtatatgatataggcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
|||||||||||||||||||||||||| ||||| | || |||| || ||
--nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTAN-TACTTGACCAGTTC-----------------------------------------------
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02020.t01 (Vitis vinifera), 3'ss of exon 4
--------atgagtgga--gttgcactttaatgtatatgatatag-gcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
| | || | ||| | |||| | | |||| | | | | |||| || | | | || || || ||| | || | | | |||||| ||||||||||| |||||||||||||| ||||| | ||| |||| || || |||||||||| || || || |||| |||||||| |||||||| |
ccattcccaccattgaattattggattttagtct-tatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgttcaata----------tgtagGTTTTGATGGAGTCGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02080.t01 (Vitis vinifera), 3'ss of exon 4
atgagtggagttgcactttaatgtatatgatataggcatgatgttaaactgg----gattttcgaattaagttcatcaattcc-taaccacaattg--caat-tgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
||| || | || ||| || || || ||||| | ||||| | | || ||| | || | |||| | ||| |||| |||||| |||||||||||||||||||||||||| ||||| | ||| |||| || || |||||||||| || ||||| |||| || ||||| || ||||| |
-------ctattgaaccatttcgtggatgtaattccca-aatactaaaccgcacttgatttgcccttcaatttctttgatgcaataacattacttgttcaatatgtagGATTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAACGATCGAACTGATAAATATGGCGGATCCCT
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02010.t01 (Vitis vinifera), 3'ss of exon 4
atgagtggagttgcactttaatgtatatgatataggcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
|| | | || |||| | | || | | | || | | || | || | || | | || | | | |||| ||||||||||||||||||||||| || ||||| | |||| |||| || || |||||||||| || || || |||||||||| || |||||||||
----gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgat-gcactaatga--taatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGAGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCACA
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02070.t01 (Vitis vinifera), 3'ss of exon 4
atgagtggagttgcactttaatgtatatgatataggcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
|| | | || |||| | | || | | | || | | || | || | || | | || | | | |||| |||||||||||||||||||||||||| ||||| | |||| |||| || || |||||||||| || || || |||||||||| || |||||||| |
----gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgat-gcactgatga--taatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCCCT
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02060.t01 (Vitis vinifera), 3'ss of exon 4
--------atgagtgga--gttgcactttaatgtatatgatatag-gcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
| | || | ||| | |||| | | |||| | | | | |||| || | | | || || || ||| | || | | | |||||| |||||||||||||||||||||||||| ||||| | ||| |||| || || |||||||||| || || || |||| |||||||| |||||||| |
ccattcccaccattgaattattggattttagtct-tatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgttcaata----------tgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02050.t01 (Vitis vinifera), 3'ss of exon 3
atgagtggagttgcactttaatgtatatgatataggcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
|| | | || |||| | | || | | | || | | || | || | || | | || | | | |||| ||||||||||||||||||||||| || ||||| | |||| |||| || || |||||||||| || || || |||||||||| || ||||||||| |
----gtaaattcatcctctaatacaattaatcatgaattaactttctagtcaatttcttcgat-gcactgatga--taatattgtttacccaatatatagGTTTTGATGGAGTTGAGATCCATGGAGCTCATGGCTATCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACAGACAAGTATGGTGGATCACT
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02040.t01 (Vitis vinifera), 3'ss of exon 5
atgagtggagttgcactttaatgtatatgatataggcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaat-tgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT---------------
|| | | || | || | || || ||| | || | | || | || | | | | | ||| |||| |||| |||||||||||||||||||||||||| ||||| | |||| |||| ||| || || || |||||||||| || ||| ||||| |
----gtaaattcatcctctgatacaaatcat---ggcttagctttctagtcaatttcttcgatgcactgatgataatattgtttaca----caatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGA---------------CCAGGTCAATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S93_177V6.1 (Physcomitrella patens), 3'ss of exon 3
---atgagtg-gagttgcactttaatgta-tatgatataggcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
|| || | || || | | | | | ||| || | ||| | | | | || | | | || || ||| | ||| || ||||| || ||||| ||||| |||||||||||||| || ||||||||||||||||| | || |||||| ||||||| ||||||||||| |
actatttgtctaaattacatatcctgacaacggggtctgaccatcat-tcaaaatagtacccaaactgtggtttgacctggttctgttcattatt----tgacagGTTTCGATGGGGTCGAGATTCATGGTGCACATGGTTTTCTCATCGATCAATTTTTGAAAGATGGCATCAATGACAGATCAGACAAGTACGGTGGATCCAT
upper sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ20558 (Selaginella moellendorffii), 3'ss of exon 4
atgagtggagttgcactttaatgtatatgatataggcatgatgttaaactgggatt--ttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
||||||||| | || ||| || ||||| ||||| | || |||||| |||||||| ||||||||||||||||| || || | ||| || || ||||| ||||| | || ||||| ||||| || | || ||||| || ||
----------------------------------------gtgttaaactatgcttctttctttctagtttcatggg---ctaacgaaaaac-tgggtgtagGCTTTGATGGTGTTGAGATCCATGGGGCTCACGGCTATCTGATCGACCAATTCCTGAAAAATGGTGTCAACGATAGAACGGATGAGTATGGTGGTTCTTTMapped 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|37994582|gb|CF806278.1|CF806278EST: TGATATCGTCAATGAATTCAGACTTGCAGCAAGGAATGCTATTGAAGCAG GGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAAT
genomic: TGATATCGTCAATGAATTCAGACTTGCAGCAAGGAATGCTATTGAAGCAGgtaaataacc ... gcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAAT
EST:
gi|151401890|gb|EV271703.1|EV271703EST: TGATATCGTCAATGAATTCAGACTTGCAGCAAGGAATGCTATTGAAGCAG GGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAAT
genomic: TGATATCGTCAATGAATTCAGACTTGCAGCAAGGAATGCTATTGAAGCAGgtaaataacc ... gcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaactgggattttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
tcctaac putative branch site (score: 1)
aattaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgagtggagttgcactttaatgtatatgatataggcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
atgagtg
- - - - - -tgcactt
- - - - - - - - - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaacca