Sequence
atgc intronic sequence ATGC exonic sequencegtttgattcagagtgtttgttactgccttaaaactttattgtatacatgtttgcccaagtttaatagttttcactcagtgtttacttatgtttgtcagtgcagGCTGAGAGTGCACTCGATCAAATGGATTGGATAGAAAAGATCACTGGGGTTATTGCATCACTACTTAGTTCTCAGGTCCCTGAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13300.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 13
gtttgattcagagtgtttgttactgccttaaaactttattgtatacatgtttgcccaagtttaatagttttcactca-gtgtttacttatgtttgtcagtgcagGCTGAGAGTGCACTCGATCAAATGGATTGGATAGAAAAGATCACTGGGGTTATTGCATCACTACTTAGTTCTCAGGTCCCTGAACAG
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------------gtatgagtacaatattgaagatgatattgtcttcatgtcgaatataattcgatatttcctatttaagtgacaccatctattttttga-gcagGCAGAGAGTGCAATAGATCAAATGGATTGGATTGAAAAGATTACTGGTGTCATTGCATCTTTGCTTAGCTCACAATCCCCAGAACAG
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GRMZM2G093670_T01 (Zea mays), 3'ss of exon 4
gtttgattcagagtgtttgttactgccttaaaactttattgtatacatgtttgcccaagtttaatagtttt-cactcagtgtttacttatgtttgtcagtgcagGCTGAGAGTGCACTCGATCAAATGGATTGGATAGAAAAGATCACTGGGGTTATTGCATCACTACTTAGTTCTCAGGTCCCTGAACAG
|| || ||| | || | | | ||| | |||| | || |||| || || | || | | | ||||||| ||||||||| | ||||| ||||||||||| |||||||| ||||| |||||||| | | || | || || ||| ||||||
--------------gtacaccacatgtttatgg---tgcagtctgccttattgattctgattaagatttcaatactccatgaacacatctgctattta-tgcagGCAGAGAGTGCAGTAGATCAGATGGATTGGATTGAAAAGATAACTGGTGTTATTGCCCCTTTGCTGAACTCACAATCCCCAGAACAG
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 13
gtttgattcagagtgtttgttactgccttaaaactttattgtatacatgtttgcccaagtttaatagttttcactcagtgtttacttatgtttgtcagtgcagGCTGAGAGTGCACTCGATCAAATGGATTGGATAGAAAAGATCACTGGGGTTATTGCATCACTACTTAGTTCTCAGGTCCCTGAACAG
| ||| | |||||| || || || | | ||| | ||| || ||||||| || | ||| ||||| |||||||||||||| |||||||| || || |||||||||||||| ||||| |||||||| |||||||| ||| |||| ||||||||| | ||||| |
--gttatttaatgtgttttttggatttttttttaattcatacaaggatggtgattaaagctttatagttt-----cattccttaattatgcttgtcagtgcagGCAGAGAGTGCGCTGGACCAAATGGATTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAGATTCCTGATAGG
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 13
gtttgattcagagtgtttgttactgccttaaaactttattgtatacatgtttgcccaagtttaatagttttcactcagtgtttacttatgtttgtcagtgcagGCTGAGAGTGCACTCGATCAAATGGATTGGATAGAAAAGATCACTGGGGTTATTGCATCACTACTTAGTTCTCAGGTCCCTGAACAG
| ||| | ||||| ||| || || | | || ||| | ||| || ||||||| || | ||| ||||| |||||||||||||| ||||||||||| || |||||||| ||||| ||||| |||||||| |||||||| ||| |||| |||||||| | |||||| |
--gttatttaatgtgttctttagatttttttaattca--tacatggatggtgattaaagctttatagttt-----cattccttaattatgcttgtcagtgcagGCAGAGAGTGCACTGGACCAAATGGACTGGATTGAAAAAATCACTGGTGTTATTGCTTCATTACTGAGTTCTCAAATTCCTGAAAGG
upper sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 13
----------------------------------------------------------------------------gtttgattcagagt---gtttgttactgccttaaaactttattgt-atacatgtttgcccaagttt-----aatagttttcactcagtgtttacttatgtttgtcagtgcagGCTGAGAGTGCACTCGATCAAATGGATTGGATAGAAAAGATCACTGGGGTTATTGCATCACTACTTAGTTCTCAGGTCCCTGAACAG
|||| || | || || ||||| || | ||||| | | || | ||| | |||| ||| | | | ||| | || ||||||| ||||| ||||||||||| || |||||||||||||| |||||||| || ||||||||||| ||| |||| |||||||||| ||||| |
gtaaatcttacagcttaggttgcactcatgaagttcagtttacttctttgaaattatttgatacctgaaactgtatttttgcttgatggttctgtgaaatactgatggaatggtgaattgttaagtgttattattgatttttttctcactagtgctcattaatgttgtacatttgcttgtcagcacagGCAGAGAGTGCACTGGACCAAATGGATTGGATTGAAAAGATAACAGGGGTTATTGCTTCATTACTGAGTTCTCAGGCTCCTGAGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgcccaagtttaatagttttcactcagtgtttacttatgtttgtcagtgcagGCTGAGAGTGCACTCGATCAAATGGATTGGATAGAAAAGATCACTGGGGTTATTGCATCACTACTTAGTTCTCAGGTCCCTGAACAG
gtttaat putative branch site (score: 4)
aagtttaatagtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgattcagagtgtttgttactgccttaaaactttattgtatacatgtttgcccaagtttaatagttttcactcagtgtttacttatgtttgtcagtgcagGCTGAGAGTGCACTCGATCAAATGGATTGGATAGAAAAGATCACTGGGGTTATTGCATCACTACTTAGTTCTCAGGTCCCTGAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA