Sequence
atgc intronic sequence ATGC exonic sequence...tccgctttctgcaagtattgaaatacaattactaaataagtgagactttgttaaattgttattataatctgtattgtgtcttatgttttttgtatttcagCTCTTAGGAAAGAGTAGTGGATTTCAAGTAGCATCAACACATCGGCCTTGTACCAAAGGGCTTTGGTTGTGGAGTGCACCTTTGAAGAAGACTGCTCTTG
Basic information
species | Glycine max |
transcript | GLYMA13G24260.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G24260.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G031053_T01 (Zea mays), 3'ss of exon 1
-tccgctttctgcaagtattgaaatacaattactaaata-agtgagactttgttaaattgttattataatctgtattgtgtcttatgttttttgtatttcagCTCTTAGGAAAGAGTAGTGGATTTCAAGTAGCATCAACACATCGGCCTTGTACCAAAGGGCTTTGGTTGTGGAGTGCACCTTTGAAGAAGACTGCTCTTG
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tcatactcatactcagctttaatataagttgattttttatagtgcattattttttgttaatcctctgcatcagt-tgataaaatccatcctctatatg-cagCTTCTTGGGCGAAGCGGCGGGTTTCAAGTGGCTTCAACACATCGGCCTTGCACCAAAGGACTTTGGATGTGGAGTGCGCCTTTGAAGAGAACTGGTCTGG
upper sequence: GLYMA13G24260.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G098129_T01 (Zea mays), 3'ss of exon 1
tccgctttctgca-agtattgaaatacaattactaaataagtgagactttgttaaattgttattataatctgtattgtgtcttatgttttttgtatttc--agCTCTTAGGAAAGAGTAGTGGATTTCAAGTAGCATCAACACATCGGCCTTGTACCAAAGGGCTTTGGTTGTGGAGTGCACCTTTGAAGAAGACTGCTCTTG
| | | | || || | ||| | | | ||| || || ||||| | || |||| || | || || | |||| | || || || || |||||||| || ||||||||||| ||||| || || || |||||| |||||||| | |||||||||| |||| | | |
tataccccatacctagctttaatataagttgatgttctttcatcgacgttattt--ttgtt-taattctctgcatcacttgataaaattgacactctatgtagCTTCTTGGGCGAAGCAGCGGTTTTCAAGTGGCTTCAACACATCGTCCTTGCACAAAGGGACTTTGGATGTGGAGTACGCCTTTGAAGAGAACTGGTTTGG
upper sequence: GLYMA13G24260.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G46070.1 (Arabidopsis thaliana), 3'ss of exon 1
-----tccgctttctgcaagtattgaaatacaattactaaataagtgagactttgttaaattgt-tattataatctgtattgtgtcttatgttttttgtatttcagCTCTTAGGAAAGAGTAGTGGATTTCAAGTAGCATCAACACATCGGCCTTGTACCAAAGGGCTTTGGTTGTGGAGTGCACCTTTGAAGAAGACTGCTCTTG
| | || | | | | | || | | | | | |||| ||| | | ||| ||| ||||| |||| | || || |||| | ||| |||| ||| |||||||||||||||||||| ||| |||||||| |||||||||||||||||| | ||| | || | || |||||||
ttatgtttgtttgatttggttctgtgtacattgttttgaggtcta-gggtttatgtttctgtgtgtttcttaaattgttttgtg----gtgttgtgcgt-ttgtagCTTCTTGGACGCAGTAATGGGTTTCAAGTAGCATCAACACACAAGCCGTGTACCAAGGGGCTTTGGTTGTGGAGTTCTCCTATAAAAAGAACAGCTCTTG
upper sequence: GLYMA13G24260.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0003g00370.t01 (Vitis vinifera), 3'ss of exon 1
------tccgctttctgcaagtattgaaatacaattactaaataagtgagactttgttaaattgttattataatctgtattgtgtcttatgttttttgtatttcagCTCTTAGGAAAGAGTAGTGGATTTCAAGTAGCATCAACACATCGGCCTTGTACCAAAGGGCTTTGGTTGTGGAGTGCACCTTTGAAGAAGACTGCTCTTG
|| || || || || | || || | || | ||||| | ||| | || || | || ||| | || | || |||| | || | ||||||||| |||||||| |||||||| |||||||| |||||||||||||||||||||||||| |||| || |||| ||||||||||
aagtgtacctctctcctcattctttcctgttatatatctgtacaaa--atgttttgtgtcacatctataactatgtgcactg---cttgcatgcatt-tgttgtagCTTCTTGGGAGGAGTAGTGGGTTTCAAGTTGCATCAACTCATCGGCCATGTACCAAAGGGCTTTGGTTGTGGAGCACACCCTTAAAGAGAACTGCTCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttgttaaattgttattataatctgtattgtgtcttatgttttttgtatttcagCTCTTAGGAAAGAGTAGTGGATTTCAAGTAGCATCAACACATCGGCCTTGTACCAAAGGGCTTTGGTTGTGGAGTGCACCTTTGAAGAAGACTGCTCTTG
tgtttttt CT-rich tract
ttaaattgttattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccgctttctgcaagtattgaaatacaattactaaataagtgagactttgttaaattgttattataatctgtattgtgtcttatgttttttgtatttcagCTCTTAGGAAAGAGTAGTGGATTTCAAGTAGCATCAACACATCGGCCTTGTACCAAAGGGCTTTGGTTGTGGAGTGCACCTTTGAAGAAGACTGCTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - -tgcaagt
- - - - - - - - - -gaaatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtctt