Sequence
atgc intronic sequence ATGC exonic sequencegttagtgttcctgacaatcaaaaacctcatttaagacataaaatgtttgatctttctcagaattttgggtttgttgttgcagACATCTCTACATGGAAGCTGTCCTGTTATCAAGGGTGAGAAATGGGTTGCCACCAAATGGATAAGAGACCAAACATATGATTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G23096.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G23096.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g55380.1 (Oryza sativa), 3'ss of exon 7
-gttagtgttcctgacaatcaaaaacctcatttaaga-------------cataaaatgtttgatcttt---ctcagaattttgggtttgttgtt-gcagACATCTCTACATGGAAGCTGTCCTGTTATCAAGGGTGAGAAATGGGTTGCCACCAAATGGATAAGAGACCAAACATATGATTGA-----------------
|||||| || || |||| || ||| ||| || | ||||| ||| || ||| |||| | |||| |||||||||||| ||||| ||||| || || ||||| || || |||||||| ||||| |||||||| |||||| | | || | |
tagatgtgttcgggaaaaaaaaaatactgattctagatggctttgcacgccaggcatcgtttgggattttaactttatattgtgggcgtactgtttgcagACATCTCTTCATGGTAGCTGCCCAGTGATCAAAGGAGAAAAATGGGTCGCCACAAAATGGATTAGAGACAAGA-GTAAGGCAGTGTAAATGTGGTATAGGA
upper sequence: AT2G23096.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G348578_T01 (Zea mays), 3'ss of exon 7
-----------gttagtgttcctgacaatcaaaaacctcatttaagac-----ataaaatgtttgatctttctcag--aattttgggtttgttgttgcagACATCTCTACATGGAAGCTGTCCTGTTATCAAGGGTGAGAAATGGGTTGCCACCAAATGGATAAGAGACCAAACATATGATTGA------------------
| | || ||| || ||||| || || ||||| | || | |||| || ||| |||||| || || ||||| ||||| || || ||||| || ||||||||||| |||||||||||||| |||||| || ||| | ||
gaggtagtaaaaaaattctttgcgacgccatggaaatcaatttagagttaccaatggaagtcttgatgctgctaacttgcatttgcacatgctgtcgcagACTTCACTTCATGGTAGCTGCCCCGTCATCAAAGGCGAGAAATGGGTCGCCACCAAATGGATCAGAGAC--AATATAGTGTAGAAATCGAAAGGCTCAGGTG
upper sequence: AT2G23096.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S19_322V6.1 (Physcomitrella patens), 3'ss of exon 9
--------gttagtgttcctgacaatcaaaaacctc----------atttaagacataaaatgtttgatctttctcagaattttgggtttgttgttgcagACATCTCTACATGGAAGCTGTCCTGTTATCAAGGGTGAGAAATGGGTTGCCACCAAATGGATAAGAGAC-CAAACATATGATTGA----------------
|||| | | || |||| || || | | ||| ||| | || | || | |||| |||| ||||||||||| ||||| ||||| || ||||||||||||||||| || ||||| | || | ||| || ||||
ttcgattgtttagaataaattccagctaaaattttcccgtagttatgcttgcaaatcatcatgacagattctcacttgattgcaactttctccgcaacagAGCGCTCTGCATGGAAGCTGCCCTGTAATCAAAGGCGAGAAATGGGTTGCCACAAAGTGGATTCGCAACACTGACAAATT-TTGATCACCACCATGCGAAC
upper sequence: AT2G23096.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S172_91V6.1 (Physcomitrella patens), 3'ss of exon 8
-------gttagtgt--tcctgacaatcaaaaacctcatttaagacata---------aaatgtttgatctttctcagaattttgggtttgttgttgcagACATCTCTACATGGAAGCTGTCCTGTTATCAAGGGTGAGAAATGGGTTGCCACCAAATGGATAAGAGAC-----CAAACATATGATTGA-----------
||| |||| ||| || | || || || | | |||| | || || ||||| | | |||||||||||||| |||||||| || || |||||||| ||||| || |||||| | | |||| | |||
attatttcttaacaccctccttacatcagttgtttgtgctttggttatgcttggcgatgaacgtgcaaaccttcttgttctaatgtcttcccaacaacagACCGCATTGCATGGAAGCTGTCCAGTTATCAAAGGCGAAAAATGGGTCGCCACGAAGTGGATACGCAATACCGACAAATTTTAATCTGAAAGATCCCACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttaagacataaaatgtttgatctttctcagaattttgggtttgttgttgcagACATCTCTACATGGAAGCTGTCCTGTTATCAAGGGTGAGAAATGGGTTGCCACCAAATGGATAAGAGACCAAACATATGATTGA
gtttgat putative branch site (score: 5)
ataaaatgtttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgttcctgacaatcaaaaacctcatttaagacataaaatgtttgatctttctcagaattttgggtttgttgttgcagACATCTCTACATGGAAGCTGTCCTGTTATCAAGGGTGAGAAATGGGTTGCCACCAAATGGATAAGAGACCAAACATATGATTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA