Sequence
atgc intronic sequence ATGC exonic sequencegtagatagataattgatccagaaattggtggctttaaagacatttctgttcctgtctttcaaaactaaatgttgtcttgttttagGATTGCTGTTTACAAAGCTCTCTACCGACTTTTTGGAGGCTTTGTAGCTGATGTGGTGGCTGCCATTGATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G30020.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 5
gtagatagataattgatccagaaattggtggctttaaagacatttctgttcctgtctttcaaa-actaaatgttgtcttgt-tttagGATTGCTGTTTACAAAGCTCTCTACCGACTTTTTGGAGGCTTTGTAGCTGATGTGGTGGCTGCCATTGATCAG
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gt-gaggaatgacgccccccctaattg-----ttcaa-----cttctgatgaaaaccgggaagtacttgatgtttttttgtcttcagGATTGCTGTGTACAAAGCACTCTATAGACTCTTTGGAGGATTTATTGCTGATGTAGTTGCTGCAATTGATCAG
upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 4
--gtagatagataattgatccagaaattggtggctttaaagacatttctgttcctgtctttcaaaactaaatgttgtcttgttttagGATTGCTGTTTACAAAGCTCTCTACCGACTTTTTGGAGGCTTTGTAGCTGATGTGGTGGCTGCCATTGATCAG
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gtgaggaataataaccctttgttgttttaaaactgggaattacagtcctttctgttgcattagacatttggtgtatcctt--ttcagGATTGCTGTGTACAAGGCACTCTATAGACTGTTTGGAGGGTTTGTTGCAGATGTAGTTGCTGCAATTGATCAG
upper sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 5
--gtagatagataattgatccagaaattggtggctttaaagacatttctgttcctgtctttcaaaactaaatgt-tgtct---tgt-tttagGATTGCTGTTTACAAAGCTCTCTACCGACTTTTTGGAGGCTTTGTAGCTGATGTGGTGGCTGCCATTGATCAG
| | | | ||| | | | | || || ||||| | ||| ||||||| | ||| | ||| || ||| ||||||| ||||| || |||||||| ||||||||||| ||||| || |||||||| ||||| |||||||||
gtgagggttaacaatctttgtatcttattcaaattactcagtatcatcctttcctctatttaaaaactatcttcctgtttggatgtattcagGGTTGCTGTATACAAGGCACTCTACCGGCTTTTTGGAGGTTTTGTTGCAGATGTGGTAGCTGCAATTGATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttaaagacatttctgttcctgtctttcaaaactaaatgttgtcttgttttagGATTGCTGTTTACAAAGCTCTCTACCGACTTTTTGGAGGCTTTGTAGCTGATGTGGTGGCTGCCATTGATCAG
aactaaa putative branch site (score: 2)
tcttgtttt putative PPT
tttcaaaactaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatagataattgatccagaaattggtggctttaaagacatttctgttcctgtctttcaaaactaaatgttgtcttgttttagGATTGCTGTTTACAAAGCTCTCTACCGACTTTTTGGAGGCTTTGTAGCTGATGTGGTGGCTGCCATTGATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG