Sequence
atgc intronic sequence ATGC exonic sequencegtaatagtcatactaatttccttttgtaatctgtatatatcctcatattcattacgctgattgcttattacagACAAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATC
Basic information
species | Glycine max |
transcript | GLYMA04G01470.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 5
gtaatagtcatactaatttccttttgtaatctgtatatatcctcatattcattacgctgattgcttatta----cagACAAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATC
||| | | || || || | || ||| || | | | | ||||||| ||| ||||||| ||||| || |||||||||||||| || || ||||||||||||||||||||| || ||||| |||||||||| || | | | || || |
gta-cacttcta-tagttctatacgaaaaaaaacataattcttttcggaagtcaaaaactgtacttattatatgcagGCAAATCCAGAAATCGTGAAAAGATGGAGCAACGAAGTGCAGGAAGCTGTTCAATCAAGATTTGCACTTGTGCAATTTCATGGCCTAGCTCTTCTTCACC
upper sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 5
------------------gtaatagtcatact--aatttccttttgtaatctg-tatatatcctcatattcattacgctgat-tg--cttatt----acagACAAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATC
|| | | | | | |||| | | || | | | | ||||| | | || | | | || ||||| ||||||| ||| ||| |||| ||||| ||||||||||| |||||||| ||||| || || ||||| || ||||| ||||||||||| || | | | || || |
gtatgtgcaaaacgtttagtctttgcctttatgcaattgcatattacagccagacccaaatccttacaaatgttttgtttgtatggttttattctgagcagACAAGTCCAGAAGTTGTGAAAAGGTGGAGCAATGAAGTTCAGGAGGCTGTACAGTCGAGAGCTGCTCTTGTTCAATTTCATGCCCTTGCTCTTCTTCACC
upper sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G012501_T03 (Zea mays), 3'ss of exon 4
--------------gta-atagtcatactaatttccttttgtaatctgtatatatcctcatattcattacgctgattgcttattacagACAAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATC
|| | |||| || || | || | || || | | || | | || | | ||||| |||| || |||||||| |||||||||||||| || |||||||||||||| ||||||||||| | ||||| || ||||||| || | | | || || |
gtactagcataattctatgcatatataccgatctcttgtttaaggttggtta-actgtatcttttgtgagtttgtctacactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC
upper sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 5
----------------------------gtaatagtcatactaatttccttttgta-atctgtatatatcctcat-attcattacgc-tgattgc-ttatta-cagACAAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATC
| | ||| | | || || | || || |||| | || || || | | || ||| ||||| ||||| | ||| ||| |||||||||||||||||||||| ||||| || ||||| || |||||||| || ||||| ||||||||||| || | | | || || |
gtatgtcctgcagttatattttgtgctccagttggatatattgttactagttggtgcagctatagatatttttattatgttttccacatgtttgtattattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACC
upper sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 5
---------------------gtaatagtcatactaatttccttttgtaatctgtatatatcctcatattcattacgctgattgc-ttatta-cagACAAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATC
| ||| | ||||| ||| | | | | | | | || || || || ||| |||| ||||||| ||| ||| |||||||||||||||||||||| ||||| || ||||| || |||||||| || ||||| || |||||||| || | | | || || |
gtatgtcctgtgctccacttggatatattgttactagtttgtggcagctttagttcttttttattatgttttccaca-tgtttgtactattggcagACAAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAGTTTCATGCCCTTGCTCTCCTTCACC
upper sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaatagt--catactaatttccttttgtaatctgta---tatatcctcatattcat-tacgctgattgcttattacagACAAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATC
||| | || || || || ||| | | | || | || | || | || |||||| || |||||||| || |||||||| ||||||||||||||||| ||||| |||| | ||||||| ||| |||||||||| || || ||||| || | |||||| ||||
gtaccttttacacaccaaaactattaggtagcttcttaattgtaatgttatgcttatattcgtatattgctgttttcagACAAACCCAGAAATTGTTAAAAGATGGAGCAATGAAGTTCAAGAAGGTATTCAATCCAGATCAGCCCTTGTTCAGTTCCATGCCCTAGCTTTGCTCCATC
upper sequence: GLYMA04G01470.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 5
------------------------gtaatagtcatactaatttccttttgtaatctgtatatatcctcatattcattacgctgattgcttatt---acagACAAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATC
| | | || | || | || | ||| || || ||| || | || | | ||| || || | ||||||| || || || || | ||| ||||| ||||| || |||||||||||||||||||| ||||| ||||| ||||||||||| || | | | |||||||
gtacaattgggttgtgtgtagattttttttattctatttatatatttaaattatcctcttacatgctctaat--aatatgattattatttttttggatagACAAACCCAGAGATAGTGAGAAGGTGGAGTAATGAAGTACAGGAAGCTGTTCAATCAAGGGCAGCACTTGTGCAATTTCATGCCCTAGCTCTCCTGCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttttgtaatctgtatatatcctcatattcattacgctgattgcttattacagACAAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATC
cgctgat putative branch site (score: 4)
taatctgtatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatagtcatactaatttccttttgtaatctgtatatatcctcatattcattacgctgattgcttattacagACAAATCCTGAAATTGTAAAAAGATGGAGCAATGAGGTTCAGGAAGCTGTTCAATCAAGAGCAGCCCTTGTACAATTTCATGCACTGGGTTTGCTGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC