Sequence
atgc intronic sequence ATGC exonic sequencegttagtactgcattatattctatgactatgtttatactttgactgctccactaggtttgggataagttcaaaagaaattaaatctgcttcaaaactgtgattgttgagttaaggtttatatttgatttcctctatagGTAATTGACTTCCATCAAACAGTTGAAGTGAATGGCATAAAGTTCTGGTGTTACACGGCAGGCCATGTTTTGGGTGCAGCCATGTTTATGGTGGATATAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G61010.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G61010.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G20140.1 (Glycine max), 3'ss of exon 1
gttagtactgcattatattctatgactatgtttatactttgactgctccactaggtttgggataagttcaaaagaaattaaatctgcttcaaaactgtgattgttgagttaaggtttatatttgatttcctctatagGTAATTGACTTCCATCAAACAGTTGAAGTGAATGGCATAAAGTTCTGGTGTTACACGGCAGGCCATGTTTTGGGTGCAGCCATGTTTATGGTGGATATAG
| | || | || || ||| | | || ||| |||| ||||||| | | | | | || ||| | | | | ||| || ||| || |||| ||||| |||||||||||||| ||||||||||| || ||||||||||| | ||||||||||| | ||||| || ||||| ||||| || ||||
-------------tttgtttggt-acaattttttttcccaga-tgcaacacttattttggga------cggaggga----------cctctaaattccagtatatctgctaacagaaattagtga------ctgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
upper sequence: AT1G61010.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S23_196V6.1 (Physcomitrella patens), 3'ss of exon 4
gttagtactgcattatattctatgactatgtttatactttgactgctccactaggtttgggataagttcaaaagaaattaaatctgcttcaaaactgtgattgttgagttaaggtttatatttgatttcctctatagGTAATTGACTTCCATCAAACAGTTGAAGTGAATGGCATAAAGTTCTGGTGTTACACGGCAGGCCATGTTTTGGGTGCAGCCATGTTTATGGTGGATATAG
|| | | | | ||||| || |||| || | ||| | | | || || || ||| ||| | | || | | |||| ||||| || |||||||| | ||||| ||||| || ||||||||||| || ||||||||||| ||||||||||||||||| ||||| || ||||
---------------------------------atgatgaggttattt-actagattattgatatgtacttcctaaa--acagcggcatcgtgtttgcaattaagcggttgta-taaccctatgttggtgatgacagGTGATTGATTTTCATCAAACTATGGAAGTCAATGGGATTCGATTCTGGTGTTATACAGCAGGCCATGTATTGGGTGCAGCCATGTTCATGGTAGACATAG
upper sequence: AT1G61010.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S77_275V6.1 (Physcomitrella patens), 3'ss of exon 5
gttagtactgcattatattctatgactatgtttatact-ttgactgctccactaggtttgggataagttcaaaagaaattaaatctgcttcaaaactgtgattgttgagttaaggtttatatttgatttcctctatagGTAATTGACTTCCATCAAACAGTTGAAGTGAATGGCATAAAGTTCTGGTGTTACACGGCAGGCCATGTTTTGGGTGCAGCCATGTTTATGGTGGATATAG
| ||||| | | || ||| |||| || | || || || | | | || | | ||||||| | || ||||| | | |||| ||||| || |||||||| | ||||| ||||| || |||||||||||| || ||||||||||| ||||||||||| ||||| ||||| |||||||
--------------------------tgtgtttgtgttatttactaacatgctag---tgtaaactatttgaatgagttgtatcgtactctatttgggcgattgttaaacta-------tattt--tcgtgttggcagGTGATTGATTTTCATCAAACCATGGAAGTAAATGGGATTCGGTTCTGGTGTTATACAGCAGGCCATGTATTGGGTGCAGCTATGTTCATGGTTGATATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgcttcaaaactgtgattgttgagttaaggtttatatttgatttcctctatagGTAATTGACTTCCATCAAACAGTTGAAGTGAATGGCATAAAGTTCTGGTGTTACACGGCAGGCCATGTTTTGGGTGCAGCCATGTTTATGGTGGATATAG
atttgat putative branch site (score: 5)
tttcctctat CT-rich tract
tttatatttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtactgcattatattctatgactatgtttatactttgactgctccactaggtttgggataagttcaaaagaaattaaatctgcttcaaaactgtgattgttgagttaaggtttatatttgatttcctctatagGTAATTGACTTCCATCAAACAGTTGAAGTGAATGGCATAAAGTTCTGGTGTTACACGGCAGGCCATGTTTTGGGTGCAGCCATGTTTATGGTGGATATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA