Sequence
atgc intronic sequence ATGC exonic sequence...tatgattttatcttaaagttaagatgtaagacatttctgaaaggtaattctagttaataaagacagatttatcgttaacaaacatttcttctttgaacagTTTGCCCAACAACTCTAAAAAGGATATGCAGACAACATGGAATTTCAAGATGGCCATCCCGAAAGATAAATAAAGTGAATCGTTCGTTAAAGAAGATACA
Basic information
species | Glycine max |
transcript | GLYMA11G13390.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G13390.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g41850.1 (Oryza sativa), 3'ss of exon 5
---------tatgattttatcttaaagttaagatgtaagacattt-ctgaa-------aggtaattctagttaataaag-acagatttatcgttaacaaac-----atttcttctttgaa---------cagTTTGCCCAACAACTCTAAAAAGGATATGCAGACAACATGGAATTTCAAGATGGCCATCCCGAAAGATAAATAAAGTGAATCGTTCGTTAAAGAAGATACA
|| | || | |||| | || | | || ||| ||| | || || || |||| | | | | || ||| || | || ||||||| || ||||||| ||||||||| | ||| |||||||| | || |||||||||||| |||||||||| || |||||||| || || |||||||| ||||||||||| ||
gtgagcctctagtgtctttttgtaaaatgaacttaacaaacctttactgtgttatttgatctactttatgtaaatagggtataattaaatggttgactttctgctgatgccttcttttaatattgggtgcagTTTGTCCAACAACTTTGAAACGGATATGCCGGCATCATGGAATTTCACGATGGCCATCTCGCAAGATAAACAAGGTTAATCGTTCATTAAAGAAGATTCA
upper sequence: GLYMA11G13390.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------tatgattttatcttaaagttaagatg--taagacatttctgaaaggtaat---tctagtta------ataaagacagatttatcg-----ttaacaaacatttcttctttga-acagTTTGCCCAACAACTCTAAAAAGGATATGCAGACAACATGGAATTTCAAGATGGCCATCCCGAAAGATAAATAAAGTGAATCGTTCGTTAAAGAAGATACA
| |||| | | ||| | | ||| ||| | | || || || | || | |||| ||| | || | | || || | | ||||||| || || || || |||||||||||||||||||||||||| ||||| |||||||| || |||||||| || || || || || |||||||||| ||
gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattccttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
upper sequence: GLYMA11G13390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
------------------------------------------------tatgatttt----atcttaaagttaagatgtaagacatttctgaaagg--taattctagttaataaagacagatttatcgttaacaaacatttct---tctttgaacagTTTGCCCAACAACTCTAAAAAGGATATGCAGACAACATGGAATTTCAAGATGGCCATCCCGAAAGATAAATAAAGTGAATCGTTCGTTAAAGAAGATACA
| || || | | ||| ||| | ||||| || | || | || | || || | ||| | | ||||||| ||||||||| | ||| | ||||||||||||||||||||||| ||||||||||| ||||||||||| || || || ||||| | |||||||| |
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgcagctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccattgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA
upper sequence: GLYMA11G13390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G105004_T01 (Zea mays), 3'ss of exon 4
------------------------------------------------tatgatttt----atcttaa--agttaagatgtaagacatttctgaaaggtaattct---agttaataaag-acagatttatc---gttaacaaacatttcttctttga-------acagTTTGCCCAACAACTCTAAAAAGGATATGCAGACAACATGGAATTTCAAGATGGCCATCCCGAAAGATAAATAAAGTGAATCGTTCGTTAAAGAAGATACA
| ||| || | | | | | ||||| | | ||| || | |||| ||| | | | || | | | | | ||| || | | ||||||| ||||| || | ||| | ||||||||||||||||||||||| |||||||||| ||||||||||| || || |||||||| || ||||||||| |
gtgagccctactgtattgttacgaagtctctgttaaatctagatttgctgtgacattcacagtactgattactgaagata-atgccatcattgtagaagaatttcttagattaggagattatggaatgaactgcttcttctgacacttgcctataaacaccattgcagTTTGTCCAACGACATTGAAACGAATATGCAGACAACATGGAATTTCCCGATGGCCATCTCGAAAGATAAACAAGGTCAATCGTTCATTGAAGAAGATAGA
upper sequence: GLYMA11G13390.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0094g00020.t01 (Vitis vinifera), 3'ss of exon 4
tatgattttatcttaaagttaagatgtaagacatt-tctgaaaggtaattctagttaataaagacagatt--tatcgttaacaaacatttcttctttgaacagTTTGCCCAACAACTCTAAAAAGGATATGCAGACAACATGGAATTTCAAGATGGCCATCCCGAAAGATAAATAAAGTGAATCGTTCGTTAAAGAAGATACA
| | | | ||| | || |||| || | || ||| | | | || | || | ||| | | | | |||| || ||||||||||| || || || ||||| || |||||||||||||| || ||||||||||| ||||| ||||| || || ||||| | || | | |||||||||
agtagtcccaacaactagtataaat--aagatgttatttggaagaagaagttggcaaactgtg-tagtctgatattgattttgattttatctttgttttacagTTTGCCCCACTACACTCAAAAGAATCTGCAGACAACATGGGATATCAAGATGGCCGTCCCGCAAGATCAACAAGGTGAACAGATCACTGAGGAAGATACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattctagttaataaagacagatttatcgttaacaaacatttcttctttgaacagTTTGCCCAACAACTCTAAAAAGGATATGCAGACAACATGGAATTTCAAGATGGCCATCCCGAAAGATAAATAAAGTGAATCGTTCGTTAAAGAAGATACA
cgttaac putative branch site (score: 3)
catttcttcttt putative PPT
tagttaataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgattttatcttaaagttaagatgtaagacatttctgaaaggtaattctagttaataaagacagatttatcgttaacaaacatttcttctttgaacagTTTGCCCAACAACTCTAAAAAGGATATGCAGACAACATGGAATTTCAAGATGGCCATCCCGAAAGATAAATAAAGTGAATCGTTCGTTAAAGAAGATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - ctgaaag