Sequence
atgc intronic sequence ATGC exonic sequence...ttgccttaaatttgaaaactgtttaaaccttttatgatgactttttagttgatgtacatgcatttattcttgagttctaatttttagttaccatttgcagAAAATGTATTCAATCTTTGCAGCTTGCCTAATCTAGAAGGAATGACATATAGGCAAATAAGACATAGATTTCAAGAA
Basic information
species | Glycine max |
transcript | GLYMA20G35310.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35310.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G43745.1 (Arabidopsis thaliana), 3'ss of exon 12
ttgccttaaatttgaaaactgtttaaacctt--ttatgatgactttttagttgatgtacatgcatttattcttgagttctaatttttagt-taccatttgcagAAAATGTATTCAATCTTTGCAGCTTGCCTAATCTAGAAGGAATGACATATAGGCAAATAAGACATAGATTTCAAGAA
| | | || | | || | || | | || ||||||||| |||| || | | | | | |||| ||| ||| |||||||||||||||| |||||||||||||| || ||||||| || | | ||||| ||| |||||| | || || ||
gtacggtgtgctttcagcttactttactgttatctgtatagaatttttagttcatgt--ttgtagtcaagactaa---ttaataccaagtctacttgttgcagAAAATGTATTTAATCTTTGCAGCTTCCCCAATCTAGTTGGGACAAAGTATAGACAACTAAGACTGGGGTTCCAGGAG
upper sequence: GLYMA20G35310.1 (Glycine max), 3'ss of exon 12
lower sequence: AT5G02940.1 (Arabidopsis thaliana), 3'ss of exon 12
ttgccttaaatttgaaaactgtttaaaccttttatgatgactttttagttgatgtacatgcatttattcttgagttctaatttttagttaccatttgcagAAAATGTATTCAATCTTTGCAGCTTGCCTAATCTAGAAGGAATGACATATAGGCAAATAAGACATAGATTTCAAGAA
| | ||| || | | ||| |||||| ||| | ||| | | | | ||| | || | | ||| |||||||||||||||| || ||||||||||| || |||||| || |||| ||||| || |||||| | || || ||
----------gtaagatactattattatacat-atgttgacttattaagttttgt---tatcaagactgattagtaccaagtctc---tactcgttgcagAAAATGTATTTAACCTTTGCAGCTTCCCCAATCTAACTGGGATGAAGTATAGACAGTTAAGACTGGGGTTCCAGGAG
upper sequence: GLYMA20G35310.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv05s0020g04630.t01 (Vitis vinifera), 3'ss of exon 12
ttgccttaaatttgaaaactgtttaaaccttttatgatgactttttagttgatgtacatgcatttattcttgagttctaatttttagttaccattt----gcagAAAATGTATTCAATCTTTGCAGCTTGCCTAATCTAGAAGGAATGACATATAGGCAAATAAGACATAGATTTCAAGAA
| | ||||| | |||||| | | | || | | | || | || | | || |||| | | | ||| |||||||||||||| ||||||| ||| || |||||||||| ||||| | ||||||||| |||||| | ||||| |||
-tccaataaatcaattttttttttaaaaaga--aaagccaatattca-tgagtttaattcttcttgatttggaaagttaatcacttcctgcttttttgttgcagAAAATGTATTTAATCTTTTCAGTTTCCCTAATCTAGCCGGAATAAAGTATAGGCAATTAAGACGTGGATTTGAAGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagttgatgtacatgcatttattcttgagttctaatttttagttaccatttgcagAAAATGTATTCAATCTTTGCAGCTTGCCTAATCTAGAAGGAATGACATATAGGCAAATAAGACATAGATTTCAAGAA
ttctaat putative branch site (score: 2)
ttctaatttttagtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgccttaaatttgaaaactgtttaaaccttttatgatgactttttagttgatgtacatgcatttattcttgagttctaatttttagttaccatttgcagAAAATGTATTCAATCTTTGCAGCTTGCCTAATCTAGAAGGAATGACATATAGGCAAATAAGACATAGATTTCAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
-tgcctta
- - - - - - - - - - - - - - - - - tgatgac
- - - - - - - - - - - - - - - - - - - - - - - -gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgca