Sequence
atgc intronic sequence ATGC exonic sequencegtttttattacacttttatctttgatcaactatgttccttgatggttgtatctgattgaaatgttgttgttttcagGTGAAAAAAGGAAGAGACTAGAAGAGGAGAAGGGGATTATCATCCGGTTTGTCATTGGTCACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G05170.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------------------gtttttattacacttttatctttgatcaactatgttccttgatggttgtatctgattgaaatgttgttgtttt----------cagGTGAAAAAAGGAAGAGACTAGAAGAGGAGAAGGGGATTATCATCCGGTTTGTCATTGGTCACAG
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gttgttgacattaaaatctggaatatgtgtttcattaagaaaaatctgtttattccatcgcaaaaaagtgaaggacagtacttttgttcccctgctgaaaagaaaaggaacagtacttctatagttttattggcatgactcgataaactaacagacaaaaaacagGTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCGTCATTGGCCACAG
upper sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G38500.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------gtttttattacacttttatctttg--atcaactatgtt--ccttgatg----gttgtatctgattgaaatgttgttgttttcagGTGAAAAAAGGAAGAGACTAGAAGAGGAGAAGGGGATTATCATCCGGTTTGTCATTGGTCACAG
||||| ||| | | ||| ||| || ||| | || || | | || | | | ||| || | || |||||| ||||| |||| | |||| || |||||||| ||||||||||| ||||| |||||||| ||
gttcataatttcatgatttttcatccttgcttcctagttattttctgctatacttttttttatatgtatattttttctgtctactttattggccgtagtttcttgtaatgtattcttgtgataacatggtacatagGTGAGAAAAGAAAGAAATTAGAGGAAGAGAAGGGCATTATCATCCGATTTGTAATTGGTCATAG
upper sequence: AT1G05170.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------gtttttattacacttttatctttgatcaactatgttccttgatggttgtatctgattgaaatgttgttgttttcagGTGAAAAAAGGAAGAGACTAGAAGAGGAGAAGGGGATTATCATCCGGTTTGTCATTGGTCACAG
|| ||| | ||| | | || ||| | | | | |||| ||| || || | | ||||||||||||||||| || || || |||||||| |||||||| || |||||||||||||| ||
gttcatggatgtttctttgctttctattcctggagttcttttttcttattcatatcttattttagcttcttattgg--atgatgtcttacgattgtttctt-ctggaacac-atggaaaatagGTGAAAAAAGGAAGAAGCTGGAGGAAGAGAAGGGCATTATCATTCGCTTTGTCATTGGTCATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatcaactatgttccttgatggttgtatctgattgaaatgttgttgttttcagGTGAAAAAAGGAAGAGACTAGAAGAGGAGAAGGGGATTATCATCCGGTTTGTCATTGGTCACAG
atctgat putative branch site (score: 4)
ttgttttc putative PPT
attgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttattacacttttatctttgatcaactatgttccttgatggttgtatctgattgaaatgttgttgttttcagGTGAAAAAAGGAAGAGACTAGAAGAGGAGAAGGGGATTATCATCCGGTTTGTCATTGGTCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA