Sequence
atgc intronic sequence ATGC exonic sequence...aaaatgaaaggattgcataagctgattttatagttacctgtaaattgattagtacaagttgtaacacgacatgtgtttgtgttttccttttgcttaaaagTTATTAGGTTCACCTGTTGATGCCAGCCTTGGATTTCTCCAAAGTGAAAATGCAAAAAGATATGTTCGCCAGCTTCCACAATATAGGAAGCAAAATTTCT
Basic information
species | Glycine max |
transcript | GLYMA11G02420.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G02420.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 4
--aaaatgaaaggat-tgcataagctgattttatagttacctgtaaattgattagtacaagttgtaacacgacatgtgtttgtgttttccttttgcttaaaagTTATTAGGTTCACCTGTTGATGCCAGCCTTGGATTTCTCCAAAGTGAAAATGCAAAAAGATATGTTCGCCAGCTTCCACAATATAGGAAGCAAAATTTCT
|| | | || |||| | | | | ||| || || || || || || | | | | |||| || || | ||||| | |||| || || | |||||| ||||| |||||||| | |||||| |||||||||||||| | || || ||||| | | | || | |||
ttaacttctattaatctgcaccattgagtacctttctcctttgttaaaatgctactataatctg-ggcattaattttaatgagttttttctcttcc--aaaagCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC
upper sequence: GLYMA11G02420.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g00270.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------aaaatgaaaggattgcataagctgattttatagttacctgtaaattgattagtacaagttgtaacacgacatgtgtttgtgttttccttttgcttaaaagTTATTAGGTTCACCTGTTGATGCCAGCCTTGGATTTCTCCAAAGTGAAAATGCAAAAAGATATGTTCGCCAGCTTCCACAATATAGGAAGCAAAATTTCT
|| | | | | | ||| | || | | || || ||| || || || | | |||| |||| | | | || | | |||||||||| |||||| || ||||| ||||||| |||| | ||||| | |||||||| | ||||||||||||||| |||||| | |||
gtatggttcttggtgcttttggagtgatgtttacttttggctgcagcattcttgtttccagttttccatgataaatcctacaaaatcagc-caatctggctcagaac-taccacaatttttttctttggtgtgacagCTTCTCGGTTCACCTGATGATGCAAGTCTTGGCTTTCTCCGAAGTAATAATGCCCGACGATATGTTAGGCAGCTTCCACAATATCCAAAGCAACAAATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattagtacaagttgtaacacgacatgtgtttgtgttttccttttgcttaaaagTTATTAGGTTCACCTGTTGATGCCAGCCTTGGATTTCTCCAAAGTGAAAATGCAAAAAGATATGTTCGCCAGCTTCCACAATATAGGAAGCAAAATTTCT
ttgtaac putative branch site (score: 2)
tttgtgttttcctttt putative PPT
ttaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaatgaaaggattgcataagctgattttatagttacctgtaaattgattagtacaagttgtaacacgacatgtgtttgtgttttccttttgcttaaaagTTATTAGGTTCACCTGTTGATGCCAGCCTTGGATTTCTCCAAAGTGAAAATGCAAAAAGATATGTTCGCCAGCTTCCACAATATAGGAAGCAAAATTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
-aaatgaaa
- - - - - - -tgcataa
- - - - - - - - - - gctgatt
- - - - - - - - - - - - - - - - - -acctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgtg