Sequence
atgc intronic sequence ATGC exonic sequence...aaaattagtagttaatcacacataagtgaaatttaaactacctatggtaaattttgcaaattaaatgctattgagactgatctggtgtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG
Basic information
species | Glycine max |
transcript | GLYMA13G19640.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g62020.1 (Oryza sativa), 3'ss of exon 3
-------aaaattagtagttaatcacacataa--gtgaaatttaaactacctatggtaaattttgcaaattaaatgctattgagactgatctggtgtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG
|| | | |||||| | | | || | || ||| | || |||| | | || | || | | | || | || | ||| | | | |||| || |||||||| ||||||||||||||||| || || |||||| | |||||||| ||||| ||||||||||||||||| |||
ttgctgcaatact-gtagttcgtattgtagcattatgtgacttcaacatctta--gtaactatagcta-ttctacgatcttttg-ctaa-ctgacttatta---tgcagGTGCGCATTGCTCGCATTTTCAATACATATGGCCCTCGAATGTGTCTAGATGATGGCCGTGTGGTTAGCAATTTTGTTGCCCAG
upper sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g17230.1 (Oryza sativa), 3'ss of exon 3
---aaaattagtagttaatcacacat-aagtgaaatttaaactacctatggtaaattttgcaaattaaatgctattgagactgatctggt--gtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG
| | || || | | | ||| | || | | |||| | | ||| || || | | | ||| || || | | |||| | ||||| ||||| ||||| |||||||| || || |||||||| ||||||||||| || |||||||| || || || |||
tttaccacatgtt-ttgtttatgtgttgagtaacatc---attgcctactgaatggtttcca--tttattaaagagaaaacttgactaacaaatgtttctcctcagGTGAGAATTGCGCGAATATTCAACACATATGGCCCTCGTATGTGTTTAGATGATGGGCGAGTTGTTAGCAACTTCGTCGCTCAG
upper sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G370048_T01 (Zea mays), 3'ss of exon 4
aaaattagtag--ttaatcacacataagtgaaatttaaactacctatggtaaattttgcaaattaaatgctattgagactgatctggtgtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG
| || | | || ||| | | || | | || || |||||| | | | | | | | || ||| | |||| |||||||| || ||||||||||||||||| || || |||||| | |||||||| ||||| || ||||||||||||||||||
tcttctggtgggataaaaaacaaaataatgcagctct--ttattagccttagattttgttatctctccttgaatatgttttcctaacttgaatagttaacagGTGCGTATTGCCCGCATTTTCAATACATATGGTCCTCGTATGTGTCTCGATGATGGCCGTGTGGTCAGCAATTTTGTTGCACAG
upper sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G359234_T03 (Zea mays), 3'ss of exon 3
aaaattagtagt-taatcacacataagtgaa-atttaaactacctatgg---taaattttgcaaattaaatgctattgagactgatctggtgtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG
|| || | | | | | || || | | | || | ||| |||| |||| | | | | | | || ||| | |||| |||||||| || ||||||||||||||||| || || ||||| | || ||||| ||||| || ||||||||||||||||||
-----taatattctggtggaataaaacaaaacactgcagctccttattagcttaaaatttgttatcactccttgaatatgttttactaacctgaatagttaacagGTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAG
upper sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G347717_T01 (Zea mays), 3'ss of exon 3
---aaaattagtagtt--aatcacacataagtgaaatttaaactacctatggtaaattttgcaaattaaatgctattgagactgatctggtgtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG
||| ||| ||| | | || | | | | ||| | | || | | || || | | ||| | |||| | | |||| | ||||| || || || || |||||||| || || |||||||| |||||||| || || |||||||| ||||||||||||
tctttgtttatatgttgcaatgatgcttacgagttgtctgtgtgctttatcttta-ttctcttcttgaagagcaa---actttgacatactgtgcttccct-cagGTGAGAATTGCACGCATATTTAACACATATGGCCCTCGAATGTGTTTAGATGATGGCCGAGTTGTTAGCAACTTTGTTGCACAG
upper sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G53520.4 (Arabidopsis thaliana), 3'ss of exon 3
aaaattagtagttaatcacacataagtgaaattta-aactacctatggt-aaattttgcaaattaa--atgctattgagactgatctggtgtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG
|| | | | | || | || | | |||| |||| |||| | | || | || | ||| | ||| | ||| ||||| | |||||||| |||||||| |||||||| ||| | ||||| | |||||||||||||| ||||| || |||||||| |||
---gtttccaatgttttgga-atgtttagaactgatgactatttatgtccaaatcacggatataacttataagagtgatctctaactgcattttcaattttcagGTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAG
upper sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0040g02710.t01 (Vitis vinifera), 3'ss of exon 4
----aaaattagtagttaatcacacataagtgaaatttaaactacctatggtaaattttgcaaattaaatgctattgagactgatctggtgtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG
| | | | | || | | || | | || | || || | | | | | || | ||| | | | | | || || |||| ||||| || || ||||||||||||||||| || || |||||| | |||||||||||||| |||||||||||||||||||||
aatgggccatccttataacttctactttactgtatagatatctccataaagtggactgtagacaatagtttggattaa---tcactgaattttctg-ttcgcagGTACGTATAGCACGGATTTTCAATACATATGGGCCTCGTATGTGTATTGATGATGGGCGTGTGGTTAGCAATTTTGTTGCACAG
upper sequence: GLYMA13G19640.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S209_52V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------------------------aaaattagtagttaatcaca---cataagtgaaatt-taaactacctatggtaaattttgcaaattaaatgctat----tgagactgatctggtgtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG
| |||| | | ||| | || | | | | | | | || | | | |||| || | | || | | ||| ||| | | ||||||| |||||||| ||||||||||| |||||||| | |||||| | |||||||| | || || ||||| || || || |||
gtacagtccgaattttcatggattttgaatatgcagtggcagtagtttacggtaagttccatttaggaagtcatcgaaggctatggattagctggtggagttctaattcgagaaatcacaaaggtgttgttttgctgcaaggtttttgaggtttgaagtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtaaattttgcaaattaaatgctattgagactgatctggtgtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG
gactgat putative branch site (score: 3)
attttgcaaattaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaattagtagttaatcacacataagtgaaatttaaactacctatggtaaattttgcaaattaaatgctattgagactgatctggtgtgatggtttatagGTTCGTATTGCTCGAATTTTCAATACATATGGACCCCGCATGTGTTTGGATGATGGGCGTGTCGTTAGCAATTTTGTTGCACAG
- - - - - - - - cacacat
- - - - - - - - - - - - - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtg