Sequence
atgc intronic sequence ATGC exonic sequencegtagtttctctttcgaatagcttctcttttatggtcttaacaatagctgtgctaagtgtttttcttgaaatggtagCCGGAGAATCTGTTGCTGACTTCAGATGGACACATTAAGATTGCGGATTTTGGAAGTGTAAAGCCGATGCAGGATAGCCAGATCACAGTTCTACCTAATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04510.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G34430.1 (Glycine max), 3'ss of exon 4
gtagtttctctttcgaatagcttctcttttatggtcttaacaatagctgtgctaagtgtt---tttcttgaaatggtagCCGGAGAATCTGTTGCTGACTTCAGATGGACACATTAAGATTGCGGATTTTGGAAGTGTAAAGCCGATGCAGGATAGCCAGATCACAGTTCTACCTAATG
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---gtagttctgtggcatgattatactgcatcattgccatatatggccatg-tgaatattaaatttcttcaactg-cagCCAGAGAACTTATTACTTACCGCTGAAGGACATATTAAAATAGCCGATTTTGGGAGTGTGAAGCCTATGCAGGATAGCCAAATAACTGTCCTTCCAAATG
upper sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G33140.1 (Glycine max), 3'ss of exon 4
gtagtttctctttcgaatagcttctcttttatggtcttaacaatagctgtgctaagtgtt---tttcttgaaatggtagCCGGAGAATCTGTTGCTGACTTCAGATGGACACATTAAGATTGCGGATTTTGGAAGTGTAAAGCCGATGCAGGATAGCCAGATCACAGTTCTACCTAATG
|| || | | || | | || | | || ||| || | | | || |||||| || || |||| ||||| | || || || | || ||||| ||||| || || |||||||| ||||| ||||| |||||||||||||| || || || || || ||||
---gtagttccgtggcatggttatactgcatcattgccatatatggctatg-tgaatattaaatttcttcaactg-cagCCAGAGAACTTATTACTTACAGCTGAAGGACATATTAAAATAGCCGATTTTGGGAGTGTGAAGCCTATGCAGGATAGCCAAATAACTGTCCTTCCAAATG
upper sequence: AT5G04510.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0074g00100.t01 (Vitis vinifera), 3'ss of exon 5
gtagtttctctttcgaatagcttctcttttatggtcttaacaatagctgtgctaagtgtttttcttgaaatggtagCCGGAGAATCTGTTGCTGACTTCAGATGGACACATTAAGATTGCGGATTTTGGAAGTGTAAAGCCGATGCAGGATAGCCAGATCACAGTTCTACCTAATG
|| ||| || | | ||| ||| || | || ||||| |||| || |||||||||| || | || ||| |||||||||| || || ||||| |||||||| ||||||||||| ||||||||||| | || || || || || ||||
--------gtattttaattgcctatacaatatttcctttgca-tgtgaaaattattaacttttcatgaattg-cagCCGGAGAACTTGCTACTTACTGCAGATGGACATATCAAAATTGCTGATTTTGGGAGTGTAAAGCCTATGCAGGATAGTCTAATTACCGTCCTTCCCAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctcttttatggtcttaacaatagctgtgctaagtgtttttcttgaaatggtagCCGGAGAATCTGTTGCTGACTTCAGATGGACACATTAAGATTGCGGATTTTGGAAGTGTAAAGCCGATGCAGGATAGCCAGATCACAGTTCTACCTAATG
tcttaac putative branch site (score: 2)
tttttcttg putative PPT
ttaacaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtttctctttcgaatagcttctcttttatggtcttaacaatagctgtgctaagtgtttttcttgaaatggtagCCGGAGAATCTGTTGCTGACTTCAGATGGACACATTAAGATTGCGGATTTTGGAAGTGTAAAGCCGATGCAGGATAGCCAGATCACAGTTCTACCTAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA