Sequence
atgc intronic sequence ATGC exonic sequence...cataccaaatatatgcatttaaatatctctgtgttcttttacattgcatcttttacttcagttatataactattcatactattcatgctgatttgtccagTGGATGGTGGATGAGAACGAACTCCGTGTAATTCATTATACACTAGGCCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATG
Basic information
species | Glycine max |
transcript | GLYMA20G37000.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G37000.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g41520.1 (Oryza sativa), 3'ss of exon 4
cataccaaatatatg-catttaaatatctctgtgttcttttacattgcatcttttact-tcagttatataactattcatactattcatgctgatttgtc-cagTGGATGGTGGATGAGAACGAACTCCGTGTAATTCATTATACACTAGGCCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATG
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--tttcagatttagaacgttttaacacct-tatgatatctcatcatatataatccacagcctgctgattatttgtaaacgtcgccttcctaactttgctgcagTGGATGGTTGATGAGAAAGAACTTAGGGTCATTCACTACACACTTGGGCCTCTTAAGCCCTGGGACTGGTGGACTGCTTGGCTTGTTAAACCTGTGGCAG
upper sequence: GLYMA20G37000.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 3
-cataccaaata-tatgcatttaaatatctctgtgttcttttacattgc-atcttttacttcagttatataactattcatactattcatgctgatttgtccagTGGATGGTGGATGAGAACGAACTCCGTGTAATTCATTATACACTAGGCCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATG
| || || | || || | | || ||| || | |||||| |||||| | | | | | || | | ||| | |||| | ||||||||||| ||||| | |||| | || ||||| || || ||||||||||||||||||||||||||||||||| | ||||| ||||||||||||||||
acgtagtggttaatttgggattggttttgattg-gtttaaaagtataactgtctttttcttcagctgtttgaatctttgtgtt-ttctcatt-atttctgcagTGGATGGTTGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATG
upper sequence: GLYMA20G37000.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 4
-----cataccaaatatatgcatttaaatatctctgtgttcttttacattgcatcttttacttcagttatataactattcatactattcatgc-tgatttgtccagTGGATGGTGGATGAGAACGAACTCCGTGTAATTCATTATACACTAGGCCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATG
|| | | || | | | | | || | || || |||| | || | | | || | |||| || || ||| || | | ||||||||||| ||||| | |||||||||| || || || ||||| ||||| ||||| || ||||| |||||||| ||||||||| | |||||||||||||
caagaaatccttagta---ggactgaggcctgcatgcttctgattgttttaaatctgccaatt--ggaaaaaaaattctcat-ctgtttatgtgtggtaaatgcagTGGATGGTAGATGAAGAAAAACTCCGTGTTATCCACTACACACTTGGCCCCCTTAAACCATGGGATTGGTGGACGTCTTGGCTTCTAAAACCTGTTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcatcttttacttcagttatataactattcatactattcatgctgatttgtccagTGGATGGTGGATGAGAACGAACTCCGTGTAATTCATTATACACTAGGCCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATG
tgctgat putative branch site (score: 3)
tttgtcc CT-rich tract
ttatataactattcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cataccaaatatatgcatttaaatatctctgtgttcttttacattgcatcttttacttcagttatataactattcatactattcatgctgatttgtccagTGGATGGTGGATGAGAACGAACTCCGTGTAATTCATTATACACTAGGCCCTCTTAAGCCTTGGGACTGGTGGACATCTTGGCTTGTGAAACCTGTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
catacca
- - - - - - -tgcattt
- - - - - - - - - - - - - - -tgtgttc
- - - - - - - - - - - - - - - - - - - - -cattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgct