Sequence
atgc intronic sequence ATGC exonic sequencegtaaatctgtgggaacatgattctacttcttcattttggttttgagaggttttcaattgatttgaccaaaatttattacagATCGAGGAAAAAACTCTTGGAAGTAAACCAGCGGCTCTACTGCTAGAAAAACTGAAGCCTCAATATTGGTTTTCAGCTCATTTACATTGCAAATTTGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G31770.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G31770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G06360.1 (Glycine max), 3'ss of exon 5
-----------------gtaaatctgtgggaacatgattctacttcttcattttggttttgagaggttttcaattgatttgaccaaaa--tttattacagATCGAGGAAAAAACTCTTGGAAGTAAACCAGCGGCTCTACTGCTAGAAAAACTGAAGCCTCAATATTGGTTTTCAGCTCATTTACATTGCAAATTTGCTG
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tcataatcatttctagagcagtcatatagatattggtttttaattacactttatatcacaacacagtttcttatttctgtacctgatatatttttgccagATAGAGGAAAAAAGACTAGGTAGTAAACCTGCTGCTGAACTTCTAGAAAAATTGAAACCACATTATTGGTTTTCAGCTCACTTACACTGCAAATTTGCTA
upper sequence: AT4G31770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G06310.1 (Glycine max), 3'ss of exon 3
-----------------gtaaatctgtgggaacatgattctacttcttcattttggttttgagaggttttcaattgatttgaccaaaa--tttattacagATCGAGGAAAAAACTCTTGGAAGTAAACCAGCGGCTCTACTGCTAGAAAAACTGAAGCCTCAATATTGGTTTTCAGCTCATTTACATTGCAAATTTGCTG
| | | | | || | || || || | || | || | ||| ||| | | | ||| | ||||| |||||||||| || || |||||||| || ||| ||| ||||||||| |||| || || ||||||||||||||||| ||||| ||||| |||||||
ttattattatttcttgagcagtcatatagatactggtttttaattacactttatataacgacacagtatcttatttctttacctgatatatttttgccagATAGAGGAAAAAAGACTAGGTAGTAAACCTGCTGCTGAACTTCTAGAAAAATTGAAACCACATTATTGGTTTTCAGCTCACTTACACTGCAAGTTTGCTG
upper sequence: AT4G31770.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g08180.t01 (Vitis vinifera), 3'ss of exon 5
------------gtaaatctgtgggaacatgattctacttcttcattttggttttgagaggttttcaattg----atttgaccaaaatttatta---cagATCGAGGAAAAAACTCTTGGAAGTAAACCAGCGGCTCTACTGCTAGAAAAACTGAAGCCTCAATATTGGTTTTCAGCTCATTTACATTGCAAATTTGCTG
|| || | | | | | ||| || ||||| || ||| | | | || |||| || |||||| |||||| |||| | ||||| || | || || |||||| ||||||||||| ||| || |||||||||||||| |||| |||||||||||||
agatgatatcttgtccttcattatacttactaattcatttcaaggaattagttttttatcattaaaaataataaaaaataaaaaacatttgctatttcagATCCAGGAAAGAACTTTGGGAAGCAAGGCTGCTGCAGAACTGCTGGAAAAACTGAAACCTTCCTACTGGTTTTCAGCTCACCTACACTGCAAATTTGCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttcattttggttttgagaggttttcaattgatttgaccaaaatttattacagATCGAGGAAAAAACTCTTGGAAGTAAACCAGCGGCTCTACTGCTAGAAAAACTGAAGCCTCAATATTGGTTTTCAGCTCATTTACATTGCAAATTTGCTG
atttgac putative branch site (score: 4)
aaaatttattaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatctgtgggaacatgattctacttcttcattttggttttgagaggttttcaattgatttgaccaaaatttattacagATCGAGGAAAAAACTCTTGGAAGTAAACCAGCGGCTCTACTGCTAGAAAAACTGAAGCCTCAATATTGGTTTTCAGCTCATTTACATTGCAAATTTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA