Sequence
atgc intronic sequence ATGC exonic sequence...ttgcaaaagccttatcttcattgattgttatagatattttaatccatttttatttctgtcaaaatttaaacatctctcacacatatataatatattgcagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAAGTTATGACGCCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
Basic information
species | Glycine max |
transcript | GLYMA14G01920.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g39640.1 (Oryza sativa), 3'ss of exon 6
---ttgcaaaagccttatcttc--attgattgttatagatattttaatccatttttatttctgtcaaaatttaaacatctctcacacatatataatatattgcagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAAGTTATGACGCCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
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gtattgtactattcagaatttctgatccatccctgcttgtactgaactcttagctagttattcttga----tcagctaaattca-atgagtgacatttgtaacagGATATGATCGAGAATGTACTAGAGATAAAAGATACACACGTCAGGGAGGTAATGACGCCTCTGGTGGATGTAGTTGCAATTGATGCTACCGCAACACTGA
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 6
ttgcaaaagccttatcttcattgattgttatagatattttaatccatttttatttctgtcaaaatttaaacatctctcacacatatataatatattgc-----agGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAAGTTATGACGCCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
||| | || |||| ||| | ||||| ||||| || || | | ||| | ||||| |||||||||||||||||||| ||||||| || || || ||||| |||| || ||||| || ||||||||||| || |||||||| || || | || || |
---------------------------gtatgagttttgtaataaatt--tgtttcta--aaaatctataccagacctatgtttatgctaccgattgccctgcagGATATGATTGAAAATGTGCTAGAGATTAAGGATACCCATGTTCGAGAGGTGATGACTCCCCTTGTTGATGTAGTCGCAATTGACGCCAGCGCCAGTCTAG
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 6
ttgcaaaagccttatcttcattgattgt-tatagatattttaatccatttttatttctgtcaaaatttaaacatctctcacacatatataatatattgcagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAAGTTATGACGCCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
| | || || | ||| ||| ||| || | | || | | || | | | || || | |||||||||||||||||||||||||||||||||||||| || || ||||| |||| || ||||| |||||||||||||| |||||||| |||| || |||||||
-------------gtatgagtttgttatatatggat-tttcgatgagtctataccat----agacttgtgatagtt------cacatgatacatattgcagGATATGATTGAAAATGTGTTAGAGATAAAGGATACGCATGTTCGAGAGGTGATGACTCCTCTTGTTGATGTAGTTGCAATAGATGGCAGCGGCAGCCTGG
upper sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 6
ttgcaaaagccttatcttcattgattgttatagatatttt---aatccatttttatttctgtcaaaatttaaacatctctcacacatatataatatattgcagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAAGTTATGACGCCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
|| | | | | | |||| || ||| ||| | | | | | ||| || || || || | ||| ||| | |||||||||||||| ||||||||||| ||||||||||| |||||||| |||||||| ||||| |||||||| |||||||||||||||||||| ||| ||| || |
ttattgacttaatgggcagaagtaaagctatacttagtttttggatctgtgtgtgtgtgtgtgtggat--aagatgctatcgctgtaata-aatctcttgcagGATATGATCGAAAATGTGTTGGAGATAAAAGATACACATGTTAGAGAAGTGATGACACCTCTTGTGGATGTTGTTGCAATTGATGCCAGTGCAACACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttatttctgtcaaaatttaaacatctctcacacatatataatatattgcagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAAGTTATGACGCCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
ctctcac putative branch site (score: 3)
acacatatataatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgcaaaagccttatcttcattgattgttatagatattttaatccatttttatttctgtcaaaatttaaacatctctcacacatatataatatattgcagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAAGTTATGACGCCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
- - - - - - - -cttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacacat