Sequence
atgc intronic sequence ATGC exonic sequence...ggctgatccaatataaaattaaagtcataactatatatatacgcatgaaaagaaaacactaactgtgtacatctgtctctattttaatgcactcattcagAAACATTATCCTCACTTGGGAGATGAAGAACTTTATCGCCATGCTAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACGATTGATTGGACTGTAG
Basic information
species | Glycine max |
transcript | GLYMA13G04410.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G04410.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g26290.6 (Oryza sativa), 3'ss of exon 6
----------------------------------------------------------------------------------------------ggctgatccaatataaaattaaagtcataact-----atatatatacgcatgaaaagaaaacactaactgtgtacatctgtctctattttaatgcactcat-tcagAAACATTATCCTCACTTGGGAGATGAAGAACTTTATCGCCATGCTAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACGATTGATTGGACTGTAG
| | | | | ||| || | | | | | || | | | | ||| | || | | | | | | | | || |||| || | |||| || | ||| |||||| | ||||| |||| | |||||| || || ||||| |||||||||||||| || |||||||||||||| |
gtaagcgaatatatcatcactattttctatttgtttagttttaggaagaatataatttgctgttcttgactagcttgccactgattgtctatttgtttagttttaggaagaatataaactgttatttaccaaaacattaatttgttttctttatgctataaatatgaagaaaagattacaaatgttttttttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCCAAATTGGTCACTTCTGCTGTTATTGCAAAGGTTCACACTATTGATTGGACTGTCG
upper sequence: GLYMA13G04410.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G312997_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------ggctgatccaatataaaattaaagtca----taactatatatatacgcatgaaaagaaaacactaac-tgtgtacatctgtctctattttaatgcactcattcagAAACATTATCCTCACTTGGGAGATGAAGAACTTTATCGCCATGCTAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACGATTGATTGGACTGTAG
|||| || ||||| | | || || | ||| || | |||| | || | | | | | |||| || | |||| || | ||| |||||| | ||||| ||||||||||||| || || ||||| |||||||||||||| || |||||||||||||| |
gtaagagaagcatcgctattattatctatttatttagtttatatgaagaatttgatgttcttgatttctttccaccgtaccgataaagctgttttttattaattaccaagacattaattttttatgctaaaatatgaagaaacaattacaaatgtccttttaatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGATATGCTAGATTGGTCACTTCTGCTGTCATTGCAAAGGTTCACACTATTGATTGGACTGTGG
upper sequence: GLYMA13G04410.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G100724_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------------ggctgatccaatataaaattaaagtcata----actatatatatacgcatgaaaagaaaacactaac-tgtgtacatctgtctct--attttaatgcactcattcagAAACATTATCCTCACTTGGGAGATGAAGAACTTTATCGCCATGCTAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACGATTGATTGGACTGTAG
|||| || ||||| | | || || | ||| || | |||| | || | | | || || | | | |||| || | || | || | ||| |||||| | ||||| |||| |||||||| || || | ||| |||||||||||||| || |||||||||||||| |
gtaagagaagcatcactattattatcatctatttgtttagtttatatgaagaatttgatgttcttgatttctttccaccgtaccgataaagctgttgtttattaattaccaagacattaattttttatgctaaaatatgaagaaacaattaaaaatgttcttttaatatctcagGAAGAACATACCAACCTATCAGACGAAGAATTATATCGGTATGCCAGATTGGTCACTTCTGTTGTCATTGCAAAGGTTCACACTATTGATTGGACTGTCG
upper sequence: GLYMA13G04410.1 (Glycine max), 3'ss of exon 5
lower sequence: AC205471.4_FGT004 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------ggctgatccaatataaaattaaagtcataactatatatatacgcatgaaaagaaa------acactaac-tgtgtacatctgtctcta--ttttaatgcactcattcagAAACATTATCCTCACTTGGGAGATGAAGAACTTTATCGCCATGCTAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACGATTGATTGGACTGTAG
|||| || |||||| | | || ||| || || | || | |||| | || | | | | | ||| | | |||| || | |||| || | ||| |||||| | ||||| ||||||||||||| || || ||||| |||||||||||||| || |||||||| |||| |
gtaagagaagcatcactattattatctatttgtttagtttatatgaagaatttgatgttcttgatttctttccaccgtaccgataaagttgttgtttattaattac-caagacattaatttttttatgctaaaatatgaagaaacaatttaaaatgttattttgatatctcagGAAGAACATCCCAACCTATCAGACGAAGAATTATATCGGTATGCTAGATTGGTCACTTCTGCTGTCATTGCAAAGGTTCACACTGTTGATTGGGCTGTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaaagaaaacactaactgtgtacatctgtctctattttaatgcactcattcagAAACATTATCCTCACTTGGGAGATGAAGAACTTTATCGCCATGCTAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACGATTGATTGGACTGTAG
ctcattc CT-rich tract
tctattttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggctgatccaatataaaattaaagtcataactatatatatacgcatgaaaagaaaacactaactgtgtacatctgtctctattttaatgcactcattcagAAACATTATCCTCACTTGGGAGATGAAGAACTTTATCGCCATGCTAGATTGGTGACCTCAGCTGTGATTGCAAAGGTTCATACGATTGATTGGACTGTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- ctgatcc
- - - - - - - -aaattaaa
- - - - - - - - - - - - - - - - - - - - - gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cactaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtac