Sequence
atgc intronic sequence ATGC exonic sequence...cttatcttcattgattgttatagatattttaatccatttttatttgtctgttaaaatttaagcatctcaaatatatatatatatatatataatattacagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAGGTTATGACACCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
Basic information
species | Glycine max |
transcript | GLYMA02G46780.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g39640.1 (Oryza sativa), 3'ss of exon 6
cttatcttcattgattgttatagatattttaatccatttttatttgtctgttaaaatttaagca------tctcaaatatatatatatatatatataatatt----acagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAGGTTATGACACCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
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-------gtattgtactattcagaatttctgatccatccctgcttgt--actgaactcttagctagttattcttgatcagctaaattca-atgagtgacatttgtaacagGATATGATCGAGAATGTACTAGAGATAAAAGATACACACGTCAGGGAGGTAATGACGCCTCTGGTGGATGTAGTTGCAATTGATGCTACCGCAACACTGA
upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 6
cttatcttcattgattgttatagatattttaatccatttttatttgtctgttaaaatttaagcatctcaaatatatatatata-tatatataatattacagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAGGTTATGACACCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
||| | || |||| || |||| | | ||||| || | || | ||| | ||| || || | ||||||||||||||||||||| ||||||| || || || ||||| ||||||| ||||| || ||||||||||| || |||||||| || || | || || |
-----------------gtatgagttttgtaataaat------ttgtttctaaaaatctatac----cagacctatgtttatgctaccgattgccctgcagGATATGATTGAAAATGTGCTAGAGATTAAGGATACCCATGTTCGAGAGGTGATGACTCCCCTTGTTGATGTAGTCGCAATTGACGCCAGCGCCAGTCTAG
upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G55930.1 (Arabidopsis thaliana), 3'ss of exon 6
cttatcttcattgattgttatagatattttaatccatttttatttgtctgttaaaatttaagcatctcaaatatatatatatatatat-ata-atattacagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAGGTTATGACACCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
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-------------------------gtatgagtttgttatatatggattttcgatgagtctataccatagacttgtgatagttcacatgatacatattgcagGATATGATTGAAAATGTGTTAGAGATAAAGGATACGCATGTTCGAGAGGTGATGACTCCTCTTGTTGATGTAGTTGCAATAGATGGCAGCGGCAGCCTGG
upper sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 6
--cttatcttcattgattgttatagatattttaatccatttttatttgtctgttaaaatttaagcatctcaaatatatatatatatatatataatattacagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAGGTTATGACACCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
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ttattgacttaatgggcagaagtaaa-gctatacttagtttttggatctgtgtgtgtgtgtgtgtggataagatgc-tatcgctgtaataaatctcttgcagGATATGATCGAAAATGTGTTGGAGATAAAAGATACACATGTTAGAGAAGTGATGACACCTCTTGTGGATGTTGTTGCAATTGATGCCAGTGCAACACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtctgttaaaatttaagcatctcaaatatatatatatatatatataatattacagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAGGTTATGACACCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
ttaaaatttaagcatc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttatcttcattgattgttatagatattttaatccatttttatttgtctgttaaaatttaagcatctcaaatatatatatatatatatataatattacagGATATGATTGAAAATGTGTTAGAGATAAAAGACACACATGTCAGAGAGGTTATGACACCTCTTGTTGATGTTGTTGCAATTGATGCAAGTTCAAGCCTGG
- - -cttcatt