Sequence
atgc intronic sequence ATGC exonic sequencegttctgtggtcgccatcttgttctttgtatttacttaatctatggatttgccaacaatctgattaactttattttctgttttagGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G24764.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 5
-------gttctgtg-gtcgccatcttgt--tctttgtatttacttaat-----ctatggatttgccaacaatctgattaactttattttctgtttta-gGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
| | || ||| || |||| ||||| | ||| || | | |||| | || ||| | | | ||| | || | ||||||||| || || | || || |||| | || || ||||||||||| |||||||||| ||| || ||| ||||||| ||||||||||||||||| |
tgtcattctcccgtacgtctgtattttgtaactcctgtatctccttgatggcatttttcaatttttctcaaactgaattgattatctttctggattaaagGAAGAAAATAAGATCTTGGACAGGCTGCACCGCCAAAAAGTTGCTGAAGTAGAAAAGCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTG
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 1
--gttctgtggtcgccatctt-gttctttgtatttacttaatctatggatttgccaacaatctgattaacttta----ttttctgtttta-------gGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
| || | || || || || | |||| | | |||||| | || || | | | ||| ||||| | |||||| |||||||| | ||||||||||| | ||||| |||||||| || |||||||| || ||||| || ||||||||||||| |||||||||| |
gtacgcgacagtggagatattcattgacactagtaactttaccagcttgtttgcccataagctaacagtatatgaggctttcctgttgcaccaaacagGAAGAGAACAAAATCTTGGATAGAATGCACCGCCAGAAAGTTGCTGAGGTTGAAAAGCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTG
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 5
----------gttctgtggtcgccatcttgttctttgtattt-acttaatctatggatttgccaacaatctgattaactttattttctgttttagGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
|| | || | ||| ||| | | | | |||| | | | | | ||||| | || || | |||||||||| |||||| | || | ||||||||| |||||||| || || || |||||||| || || || || ||||||||||||||||||| |||||||
gtattgcaatcttgtatgattattctctctcctggtgtgtgagaatcataatatgtaacttctatc--tctgactt-tgccatcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAG
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 5
-----------gttctgtggtcgccatcttgttctttgtatttacttaatctatggatttgccaacaatctgatt----aactttattttctgttttagGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
| | |||| || | | | | | ||| | || | | | | | || | | | || || | ||||||||||| |||||| | || | ||||||||| | |||||| || || || ||||||||||| || || || |||| |||||||||||||| |||||||
gtatttgcaatttcgtatggtgtttccctctccaagtatgccagccttaataatgtaatttcttatatttggttttggtatcatcatcacctctcctagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 5
---------gttctgtggtcgccatcttgttctttgtattt---acttaatctatggatttgccaacaatctgattaactttattttctgttttagGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
|| ||| | | | | | |||| || |||| ||| | || | ||| | | || | | || || | |||||||||| |||||| | || | ||||||||| | |||||| || || || ||||||||||| || || || |||| |||||||||||||| |||||||
gtatttgcaattttgta-ttgtgtttctctctcaagtatgccagacataata-atgtaatttctgacatttggtttca--tcatcacctctcccagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
upper sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 5
--------gttctgtggtcgccatcttgttctttgtatttacttaatctatgg-atttgccaacaatctgattaactt--tattttctgttttagGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
| ||| | || | ||| | | | | || || | | | |||| | || || || | |||||||||| |||||| | || | ||||||||| |||||||| || || || |||||||| || || || || |||| |||||||||||||| |||||||
gtattgcaatcttgta-tgattattct-ctctccaggtgtgtgagaaccataatatgtaacttctatcttcggactttgccatcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttacttaatctatggatttgccaacaatctgattaactttattttctgttttagGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
gattaac putative branch site (score: 2)
ctttattttctgtttt CT-rich tract
attaactttattttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctgtggtcgccatcttgttctttgtatttacttaatctatggatttgccaacaatctgattaactttattttctgttttagGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT