Sequence
atgc intronic sequence ATGC exonic sequence...agagttgtaagtgatagtggtgatttccatgcatgtccttcacaataaaattgcatccaattttgctttgcctgtaacactaatagtgtgatgtttgcagGCAGCTCAGGATGGGGTTGACATAATAAGCTTGTCTATTACTCCCAATAGACGTCCTCCTGGTGTTGCAACCTTCTTCAACCCAATAGACATGGCTTTGC
Basic information
species | Glycine max |
transcript | GLYMA09G09850.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G09850.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G052365_T01 (Zea mays), 3'ss of exon 4
----agagttgtaagtgatagtggtgatttccatgcatgtccttcacaataaaattgcatccaattttgctttgcctgtaacactaatagtgtgatgtttgcagGCAGCTCAGGATGGGGTTGACATAATAAGCTTGTCTATTACTCCCAATAGACGTCCTCCTGGTGTTGCAACCTTCTTCAACCCAATAGACATGGCTTTGC
||| | | | | | | | | | ||| |||| | | || | |||| | | ||| ||||||||| | ||| |||||||| || |||||||| |||||||| ||| | | |||||||| | ||||| |||||||| |||||||||||||| |
ataaagacctaccaacc-cactagaagcattgcaaaaggctgcagtggagaaacctgcaattgacat-gcaacacaaataactcc--ctacattgcatttacagGCAGCTGAAGATAATGTTGACATTATCAGCTTGTCCATTACTCCTAATCGGAGGCCTCCTGGACTCGCAACATTCTTCAATCCAATAGACATGGCACTCT
upper sequence: GLYMA09G09850.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G30600.1 (Arabidopsis thaliana), 3'ss of exon 5
agagttgtaagtgatagtggtgatttccatgcatgtccttcacaataaaattgcatccaattttgctttgcctgtaacactaatagtgtgatgtttgcagGCAGCTCAGGATGGGGTTGACATAATAAGCTTGTCTATTACTCCCAATAGACGTCCTCCTGGTGTTGCAACCTTCTTCAACCCAATAGACATGGCTTTGC
|||| | | | || | ||| || ||| | | | || | |||| || | | || | | ||||||||| ||||| ||||| ||||||||||||| ||| || || || || |||||||||||||||||| | || || ||||| |||||||| || ||||| ||||
------gtaactaaaaatgttacttttgtaacagaaactttgataaacagtttttcttatgtttgacatggttatg-----gatgtttt--cttttgcagGCGGCTCAAGATGGAGTTGACATAATAAACTTATCAATCACACCAAATAGACGTCCTCCTGGTATCGCTACGTTCTTTAACCCAATCGATATGGCATTGC
upper sequence: GLYMA09G09850.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv10s0092g00170.t01 (Vitis vinifera), 3'ss of exon 5
agagttgtaagtgatagtggtgatttccatgcatgtccttcacaataaaattgcatccaattttgctttgcctgtaacactaatagtg----tgatgtttgcagGCAGCTCAGGATGGGGTTGACATAATAAGCTTGTCTATTACTCCCAATAGACGTCCTCCTGGTGTTGCAACCTTCTTCAACCCAATAGACATGGCTTTGC
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--cctcaaccttgctatttgtg--ttatttgctgccttcatatggccagacaccattcacatgggcattgtaattgattttgatcttcccttttgcattcacagGCAGCTCAGGATGGAGTTGACATAGTAAGCTTGTCAATCACTCCCAACAGGCGTCCCCCTGGAATTGCAACTTTTTTTAATCCCATAGATATGGCCTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaattgcatccaattttgctttgcctgtaacactaatagtgtgatgtttgcagGCAGCTCAGGATGGGGTTGACATAATAAGCTTGTCTATTACTCCCAATAGACGTCCTCCTGGTGTTGCAACCTTCTTCAACCCAATAGACATGGCTTTGC
cactaat putative branch site (score: 2)
aatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agagttgtaagtgatagtggtgatttccatgcatgtccttcacaataaaattgcatccaattttgctttgcctgtaacactaatagtgtgatgtttgcagGCAGCTCAGGATGGGGTTGACATAATAAGCTTGTCTATTACTCCCAATAGACGTCCTCCTGGTGTTGCAACCTTCTTCAACCCAATAGACATGGCTTTGC
- - - - - - - -agtggtg
- - - - - - - - - - - - ttccatg
- - - - - - - - - - - - - - - -catgtcc
- - - - - - - - - - - - - - - - - - - - - -aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - gcatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagtgtg