Sequence
atgc intronic sequence ATGC exonic sequence...gatctctccatccttttttcttgatcccttcacccatcaaaccaaccttataatttttgttctaatcatgtgttcatatttttttttttgtgtgtggcagTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGTAGAAGGAGTTTGCTGTATAGCCTTCTGATGCCAGTGATGAGC
Basic information
species | Glycine max |
transcript | GLYMA06G40860.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G40860.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G27260.1 (Arabidopsis thaliana), 3'ss of exon 1
gatc--tctccatccttttttcttgatcccttcacccatcaaaccaaccttataatttttgtt--ctaatcatgtgttcatatttttttttttgtgtgtggcagTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGTAGAAGGAGTTTGCTGTATAGCCTTCTGATGCCAGTGATGAGC
||| | | | || | | | | | | || | | | || | || || |||| | || || |||| | | || ||| |||||| ||||||||||| || || ||||||||||| ||||||||||| ||||| ||||||| || || | || || || || ||||||| |||||||||
gattatttttcttctgggtacccaaaaggttgaaactataataactttctcaaaacttaaagaggctaacaaggt-tttatatatatgttc---tgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
upper sequence: GLYMA06G40860.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G54510.1 (Arabidopsis thaliana), 3'ss of exon 1
gatctctccatccttttttcttgatcccttcacccatcaaaccaacctt--ataatttttgttctaa---tcatgtgttcatattt---ttttttttgtgtgt-ggcagTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGTAGAAGGAGTTTGCTGTATAGCCTTCTGATGCCAGTGATGAGC
| || | || | |||| | ||| || || || || | | || || |||| | |||| | || || | | ||| |||||||||||| || || || |||||||| |||||||||||||| ||||| || |||| ||||| | || || || || ||||||| |||||| |
---------tccattcactgttaaaacctttatccaaaaagaaaatttttaatgggtctacttttatctttcatatattcacaaaagaattattgatatatgtcaacagTTCTGGGACTTCTGGTGGAGAGAGGAAACTGATGCCAACAATCGAAGAGGAACTAGACAGAAGATCACTTCTCTACAGTCTCTTGATGCCTGTGATGGAC
upper sequence: GLYMA06G40860.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0014g04690.t01 (Vitis vinifera), 3'ss of exon 1
gatctctccatccttttttcttgatcccttcacccatcaaaccaaccttataatttttgttctaatc--atgtgttcatatttttttttttgtgtgtggcagTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGTAGAAGGAGTTTGCTGTATAGCCTTCTGATGCCAGTGATGAGC
| | | | | || | ||| | | | | | | | || || ||| | | |||| ||| | || | |||| || ||||| || || || |||||||||||||||||||| || ||||||||||| | || ||| ||||| ||||| || || ||||| |||||||||
gtattgttcgttgttggtaattggggtgagaggcttttcagaatgtgtactcaaatggattgaaactgaatgcggttgctttttatttgctttgctttgcagCTCGGGGACTTCTGGCGGGGAGAGGAAGCTGATGCCAACCATAGAAGAAGAGCTGGAGAGGAGGTCATTGCTTTATAGTCTGCTCATGCCGGTGATGAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttataatttttgttctaatcatgtgttcatatttttttttttgtgtgtggcagTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGTAGAAGGAGTTTGCTGTATAGCCTTCTGATGCCAGTGATGAGC
ttctaat putative branch site (score: 2)
tatttttttttttgt putative PPT
taatcatgtgttcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatctctccatccttttttcttgatcccttcacccatcaaaccaaccttataatttttgttctaatcatgtgttcatatttttttttttgtgtgtggcagTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGTAGAAGGAGTTTGCTGTATAGCCTTCTGATGCCAGTGATGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- tctctcc
- - - - - - - - - - - - - - ttcaccc
- - - - - - - - - - - - - - - - - - tcaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtg