Sequence
atgc intronic sequence ATGC exonic sequence...tcttcattcttcctgcttgttcagtgtcataattccctactattgtggtaattctattttgtttttatcttttttactgctaatttaaattttattgtagGTGAGATTAGATCCTAGAAATAAGGAGATTGATCTTGATAGTTCAATGTATGAGAAAATTCCTGACCTAACTGAGGAAGATATGAAAAAACAAGAAGGAG
Basic information
species | Glycine max |
transcript | GLYMA07G36730.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G36730.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0077g00250.t01 (Vitis vinifera), 3'ss of exon 4
tcttcattcttcctgcttgttcagtgtcataattccctactattgtggtaattctattttgtttttatcttttttactgctaatttaaat--------tttattgtagGTGAGATTAGATCCTAGAAATAAGGAGATTGATCTTGATAGTTCAATGTATGAGAAAATTCCTGACCTAACTGAGGAAGATATGAAAAAACAAGAAGGAG
|| | | | | || || | ||| | | ||| | || || | | ||| || | | ||||| | ||||||| |||||||| | |||||||| || |||||||||||||| || |||| |||||||| |||||| | | | |||||||||||| ||||||| ||| || || |
-----gtttcttgaaaccatgtgatttgatcatctac-actgtc-taataaacttccttccttcctttttttaatatt-caaatttgggtggttctactttattgcagGTGAGAATGGATCCTAGGAACAAGGAGATTGATCTCGACAGTTTAATGTATGGAAAAATTACCCAGCGAACTGAGGAAGAGATGAAAAGACAGGAGGGGG
upper sequence: GLYMA07G36730.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0077g00200.t01 (Vitis vinifera), 3'ss of exon 3
tcttcattcttcctgcttgttcagtgtcataattccctactattgtggtaattctattttgtttttatcttttttactgctaatttaaat--------tttattgtagGTGAGATTAGATCCTAGAAATAAGGAGATTGATCTTGATAGTTCAATGTATGAGAAAATTCCTGACCTAACTGAGGAAGATATGAAAAAACAAGAAGGAG
|| | | | | || || | ||| | | ||| | || || | | ||| || | | ||||| | || |||| |||||||| | |||||||| || |||||||||||||| || |||| |||||||| |||||| | | |||||||||||||| ||||||| ||| || || |
-----gtttcttgaaaccatgtgatttgatcatctac-actgtc-taataaacttccttccttcctttttttaatatt-caaatttgggtggttctacttcattgcagGTGAGAATGGATCCTAGGAACAAGGAGATTGATCTCGACAGTTTAATGTATGGAAAAATTACCCAGCTAACTGAGGAAGAGATGAAAAGACAGGAGGGGG
upper sequence: GLYMA07G36730.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0077g00820.t01 (Vitis vinifera), 3'ss of exon 4
---tcttcattcttcctgcttgttcagtgtcataattccctactattgtggtaattctattttgtttttatcttttttactgctaatttaaattttattgtagGTGAGATTAGATCCTAGAAATAAGGAGATTGATCTTGATAGTTCAATGTATGAGAAAATTCCTGACCTAACTGAGGAAGATATGAAAAAACAAGAAGGAG
|||| | | || || | | || | | ||| || | || || |||| || || || || | ||||||| |||||||| | |||||||| || |||||||||||||| || |||| |||||||| |||||| | | |||||||||||||| ||||||| ||| || || |
gtttcttgaaaccatatgatt--tgatcatctacactgtctaataa-acaaacttccttcctttttttaatattcaaatttgggtggttctactttattgcagGTGAGAATGGATCCTAGGAACAAGGAGATTGATCTCGACAGTTTAATGTATGGAAAAATTACCCAGCTAACTGAGGAAGAGATGAAAAGACAGGAGGGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtaattctattttgtttttatcttttttactgctaatttaaattttattgtagGTGAGATTAGATCCTAGAAATAAGGAGATTGATCTTGATAGTTCAATGTATGAGAAAATTCCTGACCTAACTGAGGAAGATATGAAAAAACAAGAAGGAG
tgctaat putative branch site (score: 2)
ttttatt putative PPT
tattttgtttttatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttcattcttcctgcttgttcagtgtcataattccctactattgtggtaattctattttgtttttatcttttttactgctaatttaaattttattgtagGTGAGATTAGATCCTAGAAATAAGGAGATTGATCTTGATAGTTCAATGTATGAGAAAATTCCTGACCTAACTGAGGAAGATATGAAAAAACAAGAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - ttcttcc
- - - - - - -tgcttgt
- - - - - - - - - - -cagtgtc
- - - - - - - - - - - - - - - - - ccctact
- - - - - - - - - - - - - - - - - - - - - -tgtggta