Sequence
atgc intronic sequence ATGC exonic sequencegttagtctatttatatggtttgttttgtgttgtgttgtgagaggctgaattttgggattgactgatttgtaatttgttaaatatagGCTTGAGAAAGAGTCAGGATTCTTCTTCAATACCAAGTATTTTGATGAGAAAGTTCTAGCTGGAGAATGGGATGATGTTGAGACGTATTTGTCAGGTTTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G27030.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 1
----gttagtctatttatatggtttg--ttttgtgttgtgtt--gtgagaggctgaattttgggattgactgatttgtaatttgttaaata------tagGCTTGAGAAAGAGTCAGGATTCTTCTTCAATACCAAGTATTTTGATGAGAAAGTTCTAGCTGGAGAATGGGATGATGTTGAGACGTATTTGTCAGGTTTT
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aactaatgttctatttccttgtcacgactattatgttggattcaatggtacatttggtctagcaaggtgtaatttcctaatatggtacattctgttttagGCTTGAGCAAGAGTCAGGATTCTTCTTCAACATGAAGTACTTTGAAGAGAAGGTCCATGCTGGGGAGTGGGATGAAGTGGAGAAATATCTTTCAGGTTTC
upper sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 1
-----------------gttagtctattt---atatggtttgttttgtgttgtgttgtgagaggctgaattttgggattgactgatttgtaatttgttaaatatagGCTTGAGAAAGAGTCAGGATTCTTCTTCAATACCAAGTATTTTGATGAGAAAGTTCTAGCTGGAGAATGGGATGATGTTGAGACGTATTTGTCAGGTTTT
||| | ||| | |||| | |||| || | | | || || | ||| || || | | |||| |||||||||| |||||||||| ||||||||||||| ||||| || || ||||| || | ||||| || |||||||| || |||| || |||||||| ||
aactgatgttgtaccacgttcttttatcccagaaatggaattgcctgtgggctgatattcta--ctacatgtaataattccctacttcacattgtgttg----tagGCTTGAGCAAGAGTCAGGGTTCTTCTTCAATATGAAGTACTTCGAGGAGAAGGTCCATGCTGGGGAGTGGGATGAGGTGGAGAGATACTTGTCAGGATTC
upper sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 2
------gttagtctatttatatggtttgttttgtgttgtgttgtgagaggctgaattttgggattgactgatttgtaa--------tttgttaaatatagGCTTGAGAAAGAGTCAGGATTCTTCTTCAATACCAAGTATTTTGATGAGAAAGTTCTAGCTGGAGAATGGGATGATGTTGAGACGTATTTGTCAGGTTTT
| | || | |||| | || | | | |||| | | | ||| | | | | | | |||||||||||||| || || || |||||||||| ||||| ||||| || ||||| | ||||| |||||||| || ||||||| ||| || |||| |||
ttgaaaactctttctcttccttcctttgctaaacatttcccatttttttcattatctttgctgcttatttctttattaaaaatgtttctttctggtgcagGCTTGAGAAAGAATCTGGGTTTTTCTTCAATATGAAGTACTTTGAGGAAAAAGTACAGGCTGGTGAATGGGAAGAAGTTGAGAAGTACTTAACAGGGTTT
upper sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 1
-------gttagtctatttatatggtttgttttgtgttgt--gttgtgagaggctgaat--tttgggattgactg--atttgtaatttgttaaat-atagGCTTGAGAAAGAGTCAGGATTCTTCTTCAATACCAAGTATTTTGATGAGAAAGTTCTAGCTGGAGAATGGGATGATGTTGAGACGTATTTGTCAGGTTTT
|| ||| || | ||| | | ||| ||| | | | | | | | | |||| | | || | |||| | | ||||||||||||||||||||| || |||||||||| ||||| ||||| |||||||| | || |||||||||||||| ||||||| |||||| || || | |
tttttttttttttcttcttttccaatttacactttcttggaagtttggtgtagttaattaatcttaatttgaacggaaattattttttggtgttttgtagGCTTGAGAAAGAGTCAGGGTTTTTCTTCAATATGAAGTACTTTGAGGAGAAAGTACAGGCAGGAGAATGGGATGAAGTTGAGAAGTATTTATCCGGATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgttgtgagaggctgaattttgggattgactgatttgtaatttgttaaatatagGCTTGAGAAAGAGTCAGGATTCTTCTTCAATACCAAGTATTTTGATGAGAAAGTTCTAGCTGGAGAATGGGATGATGTTGAGACGTATTTGTCAGGTTTT
gactgat putative branch site (score: 3)
tgatttgtaatttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtctatttatatggtttgttttgtgttgtgttgtgagaggctgaattttgggattgactgatttgtaatttgttaaatatagGCTTGAGAAAGAGTCAGGATTCTTCTTCAATACCAAGTATTTTGATGAGAAAGTTCTAGCTGGAGAATGGGATGATGTTGAGACGTATTTGTCAGGTTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA