Sequence
atgc intronic sequence ATGC exonic sequence...cttttggatttgatttttgttttcaaagctactaggggtggataatcacgtggtgtaaactacgtaaatgcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTGTTCAAGATTGTAAATGAAGGTGGGTCTACACATAATCCAGATCAACAAATCAACA
Basic information
species | Glycine max |
transcript | GLYMA12G00540.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G00540.1 (Glycine max), 3'ss of exon 2
lower sequence: 13113.m00212 (Oryza sativa), 3'ss of exon 2
cttttggatttgatt--tttgttttcaaagctactaggggtggataatcacgtggtgtaaactacgtaaatgcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTGTTCAAGATTGTAAATGAAGGTGGGTCTACACATAATCCAGATCAACAAATCAACA-
| | | || || | ||| ||| | || | | || | | | | | | || |||| || || | | |||| || || |||||||||||||| ||||||||||||||| || |||||||| | | || || | | | | | | | |
ttgatagtttagaatattttcccttctcctcctctcgcatcgatcgattgcattagggtttcgaactttcacctactgatcgatcgccgactcg--ccgcagGAGGACGGATGGGTGGTGTGCAGGGTGTTCAAGAAGAAGTGCTTCTTCAAGATCGGCGGCGGCGGCGGCGGCG-AGGGGAGCGGGGGGAGCCAGGGAGGGG
upper sequence: GLYMA12G00540.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G33280.1 (Arabidopsis thaliana), 3'ss of exon 2
cttttggatttgatttttgttttca--aagctactaggggtggataatcacgtggtgtaaactacgtaaatgcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTGTTCAAGATTGTAAATGAAGGTGGGTCTACACATAATCCAGATCAACAAATCAACA-
| ||||| | | | | |||| | | | | | | || | | || | |||| || |||| || | || |||||||||| ||||| || || ||||||||||||||||| ||| ||||||| | | ||||| | ||| || | |||| | | | | | | |
-gtatggatatatatctcttattcattagaaaatttgtgaaagtcggtcg---atttttaattgaataaac-----caatctatacataa-------tgcagGAAGATGGATGGGTTGTTTGTAGAGTGTTCAAGAAGAAAAATCTGTTCAAAGTAGGGAATGATGTTGGCTCAA-ACATCAGCAATAATAGGCTTGAAGCTC
upper sequence: GLYMA12G00540.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G10350.1 (Arabidopsis thaliana), 3'ss of exon 2
cttttggatttgatttt-tgttttcaaagctactaggggt-ggataatcacgtggtgtaaactacgtaaat-gcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTGTTCAAGATTGTAAATGAAGGTGGGTCTACACATAATCCAGATCAACAAATCAACA
|| | | || || || | | | | | | | || || | ||||| || || ||| || | ||| | | | | ||||||||||||| |||||||| || |||||||| | |||||| |||||||||||| | |||||||||||| | || | ||| || | ||| ||||
--actgcactgtatattatgctgcaataaattcaatttattggttagaaatgtggtctattatatttaatccatttgcaacatattt-tatacgatcatgtagGAAGATGGATGGGTGGTATGTAGAGTGTTTATGAAGAAAAATTTGTTCAAGGTAGTAAATGAAGGTAGCTCAAGCATTAACTCATTGGACCAACACAACC
upper sequence: GLYMA12G00540.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0089g01120.t01 (Vitis vinifera), 3'ss of exon 2
-----cttttggatttgatttttgttttcaaagctactaggggtg--gataatc-acgtggtgtaaactacgtaaatgcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTGTTCAAGATTGTAAATGAAGGTGGGTCTACACATAAT-CCAG-ATCAACAAATCAACA
|| || || || | | | || | || | ||||| || | || | | | | | || || | || |||||| || |||| ||||| |||||||||||||| || |||||||||||||| | |||||| ||| || ||||| || | | |||| || | | |
gtaagtttcacaatatgcttaaggggggccataatattttccatgacgttaatctacatagttt---ccaaatgggttttttactttctaacttgtatgtatgtgcagGAGGATGGATGGGTGGTGTGCAGGGTTTTCAAGAAGAAGAACCTATTCAAGCTTGGAACCGAAGGCGGAGGAAGCAGCAGCGCCAGCATGGCCGGCTTAG-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcacgtggtgtaaactacgtaaatgcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTGTTCAAGATTGTAAATGAAGGTGGGTCTACACATAATCCAGATCAACAAATCAACA
ttatgatttatatatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttttggatttgatttttgttttcaaagctactaggggtggataatcacgtggtgtaaactacgtaaatgcttatgatttatatatgaatgtatttgtagGAAGATGGCTGGGTGGTGTGCAGAGTGTTCAAGAAGAAGAATTTGTTCAAGATTGTAAATGAAGGTGGGTCTACACATAATCCAGATCAACAAATCAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - -ggatttg
- - - - - - - - - - - - - -gctacta
- - - - - - - - - - - - - - - - - -gggtgga
- - - - - - - - - - - - - - - - - - - - - - - - -gtggtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttatg