Sequence
atgc intronic sequence ATGC exonic sequence...cttagtgattaagattgacagtttctcctttgtagttcattttcactgcataaattatataattttatcttaattcatttttttatgtgtatatatttagGTGATGCCTCCACTATGGTGCAGAATTGATAGGCTATGGTTTCCCCATCCTGGTGTTTTAGACGGGTCTATGACTAGACAACCTTTTCTCTGTCCTTTGG
Basic information
species | Glycine max |
transcript | GLYMA01G35690.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G35690.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g38930.1 (Oryza sativa), 3'ss of exon 5
cttagtgattaagattgacagtttctcctttgtagttcattttcactgcataaattatat--aattttatcttaattcattttttta----tgtgtatatatttagGTGATGCCTCCACTATGGTGCAGAATTGATAGGCTATGGTTTCCCCATCCTGGTGTTTTAGACGGGTCTATGACTAGACAACCTTTTCTCTGTCCTTTGG
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------agataacttctggaggtgtttgagagcagaattacgctgttcgatgtattgtgctcaaacttgtggacacccaatttctgactactgtttgtacttttagGTAATGCCTCCATTATGGTGCAGGCTTGATAGGATGTGGTTTGGACATCCTGGAGTTTTGGAAGGAACAATGACCAGACAACCTTTCCTCTGTCCAATGG
upper sequence: GLYMA01G35690.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G011912_T01 (Zea mays), 3'ss of exon 5
cttagtgattaagattgacagtttctcctttgtagttcattttcactgcataaattatataattttatcttaattcatttttttatgtgtatatatttagGTGATGCCTCCACTATGGTGCAGAATTGATAGGCTATGGTTTCCCCATCCTGGTGTTTTAGACGGGTCTATGACTAGACAACCTTTTCTCTGTCCTTTGG
|| | | || | ||| |||| ||| | | | | | || | || || || | | || | || ||||||| ||||||||| |||||||||| ||||||| | |||||| |||||||| ||||||| || | ||||| ||||||||||||||||| || |||
tataattttgaatggagggagtaagatttttgaagtattatcttttcgtagtgttcgtacatgttgatgccccttttctgactgcagtttgtacttttagGTAATGCCTCCATTATGGTGCAGGCTTGATAGAATGTGGTTTGGACATCCTGGAATTTTAGAGGGAACAATGACCAGACAACCTTTTCTCTGCCCACTGG
upper sequence: GLYMA01G35690.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv02s0087g00740.t01 (Vitis vinifera), 3'ss of exon 9
-cttagtgattaagattgacagtttctcctttgtagttcattttcactgcataaattatataattttatcttaattc-atttttttatgtgtatatatttagGTGATGCCTCCACTATGGTGCAGAATTGATAGGCTATGGTTTCCCCATCCTGGTGTTTTAGACGGGTCTATGACTAGACAACCTTTTCTCTGTCCTTTGG
| | |||| ||| | | ||| | ||| || | || | ||| || | | | ||| || |||||| ||| || ||||||| ||||||||||||||||||||| | |||||| |||||||||| |||||||| ||| | || |||||||| |||||||||||||||||||| |||||||
ttcctttagtattgattatttaattcatcatattagctaattgcatttgga-aattcttattatgtcttgatctttctgttcttttatttgtg-atttttagGTCATGCCTCCACTATGGTGCAGATTGGATAGGTTATGGTTTCCACATCCTGGAGTTCTTGAGGGGTCTATTACTAGACAACCTTTTCTCTGCCCTTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcataaattatataattttatcttaattcatttttttatgtgtatatatttagGTGATGCCTCCACTATGGTGCAGAATTGATAGGCTATGGTTTCCCCATCCTGGTGTTTTAGACGGGTCTATGACTAGACAACCTTTTCTCTGTCCTTTGG
tcttaat putative branch site (score: 3)
taaattatataatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttagtgattaagattgacagtttctcctttgtagttcattttcactgcataaattatataattttatcttaattcatttttttatgtgtatatatttagGTGATGCCTCCACTATGGTGCAGAATTGATAGGCTATGGTTTCCCCATCCTGGTGTTTTAGACGGGTCTATGACTAGACAACCTTTTCTCTGTCCTTTGG
cttagtg
- - - - - - - - - - - - -tcctttg
- - - - - - - - - - - - - - - - - - - - - -cactgca