Sequence
atgc intronic sequence ATGC exonic sequence...tgtttcaaagaaacttaatgatattgggttggcatgtgaaatgtcagtttcatacaataattttctgatagttatgtcaattttcaaatggtctctacagGTGATGCCTAAACAGCCAGGCTTTGAGAGGAGAGACCTTTATATGCTGTATCACTATTTAAATCATTATAATCTCTTTGGTTCCGGATACCGGTCTTCAG
Basic information
species | Glycine max |
transcript | GLYMA07G08570.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G08570.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g02640.1 (Oryza sativa), 3'ss of exon 8
tgtttcaaagaaacttaatgatattgggttggcatgtgaaatgtcagtttcatacaat--aattttctgatagttatgtcaattttcaaatggtctctacagGTGATGCCTAAACAGCCAGGCTTTGAGA---GGAGAGACCTTTATATGCTGTATCACTATTTAAATCATTATAATCTCTTTGGTTCCGGATACCGGTCTTCAG
| | || | ||| | || | || | | | | ||| | | | | | || | || | | | | | | ||||||||||| ||||||||||||||||||| |||| ||||| ||| | ||||| |||||| | || || || ||||| ||||| ||||| ||||| || |
tctgtcggatggactacagattactcaatt--ctttactactagtagtatggaaatttggagggtgtaaatgggtagtttatgctctactctgctgattcagGTGATGCCGAAACAGCCAGGCTTTGAGAAGAGGAGGGACCTGTATCTTCTGTACCACTATCTGAACCACTACAATCTTTTTGGCTCCGGGTACCGCTCAT---
upper sequence: GLYMA07G08570.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G030299_T01 (Zea mays), 3'ss of exon 8
tgtttcaaagaaacttaatgatattgggttggcatgtgaaatgtcagtttcatacaataattttctgatagttatgtca-----attttcaaatggtctct-----acagGTGATGCCTAAACAGCCAGGCTTTGAGA---GGAGAGACCTTTATATGCTGTATCACTATTTAAATCATTATAATCTCTTTGGTTCCGGATACCGGTCTTCAG
| | | || || | || | ||| || || | || ||| | || | ||| |||| | | ||| | ||| | | | || |||||||||||| ||||||||||| ||||||| |||| ||||| ||| | || || ||||| | ||||| || ||||||||||| || || ||||| || |
---tactatagaatttgaagacgtgtggtcgg----tggattgctcaattctt-cactg--tttttgatggagacatcagcagtacttttatactattactctgatacagGTGATGCCGAAACAGCCAGGGTTTGAGAAGAGGAGGGACCTCTATCTCCTCTACCACTACCTGAATCACTACAATCTCTTTGGCTCTGGCTACCGTTCAT--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtttcatacaataattttctgatagttatgtcaattttcaaatggtctctacagGTGATGCCTAAACAGCCAGGCTTTGAGAGGAGAGACCTTTATATGCTGTATCACTATTTAAATCATTATAATCTCTTTGGTTCCGGATACCGGTCTTCAG
ttctgat putative branch site (score: 3)
tctctac putative PPT
atacaataattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttcaaagaaacttaatgatattgggttggcatgtgaaatgtcagtttcatacaataattttctgatagttatgtcaattttcaaatggtctctacagGTGATGCCTAAACAGCCAGGCTTTGAGAGGAGAGACCTTTATATGCTGTATCACTATTTAAATCATTATAATCTCTTTGGTTCCGGATACCGGTCTTCAG
- - - aaagaaa
- - - - - - - - - - - - -gggttgg
- - - - - - - - - - - - - - - - catgtga
- - - - - - - - - - - - - - - - - - - - - - - - -tcataca