Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcctatcttcaagtgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G07690.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 10
----gtatgtcctatcttcaagtgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG
| |||| | || |||| || || | | || | ||| | || | | ||| || | | |||| | | | ||||||||||| ||| | ||||| || || ||||||||||||||||| || ||||| ||||||||||| |||||||| ||||| || || || |
gtaagcttgtcttccctgcaaggattattgtgt---ttactcaaagtt--ctgtt-tcctagaa-ctaaaagacttatt----ttccctgtacagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 10
gtatgtcctatcttcaagtgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG
||| ||| ||| |||| || | | | ||| | || | ||| | ||| | ||||| | | ||| | ||||| ||||| ||| | ||||| || || ||||||||||||||||| || || || ||||| ||||||||||||||||||||||| ||||| ||
gtaggtc-tat-ttcaccaaattgtttgttgtttactaaagtttggtt-ttggaaca---ctgtaaatatttct-----ttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 10
gtatgtcctatcttcaagtgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG
||| || | |||| || | | | ||| ||| ||||| | | | |||| | | ||| | ||||| ||||| ||| | ||||| || || ||||||||||||||||| || || || ||||| |||||||||||||||||| |||| ||||| ||
gtaggt--tgatttcactgaattgtttgttgtttacttaggtttagttttt----taaggctgtaaccatttct-----ttttctctacagCGCGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGCGACCTGAAGACAG
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 9
------------------------------------------------gtatgtcctatcttcaagtgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG
||| | || | || | | || | || | | | || | | | | || | | || | || |||| ||||||||||||||||| || || ||||| |||||||| ||||||||||| || |||||||| ||||| |||||||| || ||||||||
gtaagttcttcccttcctaaactgtttgtattagacagtcaatttatactatactacttgttgaggtataatcataagcttgaactccatcaactttcctttttaagtctctgattcatgttctatgcacccttt--agCGTGAGTTCTATCTTGAAGGAGGGGCCATGGTCTTGGCTGACGGAGGTGTTGTCTGCATTGATGAGTTTGATAAGATGAGGCCAGAAGATAG
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 9
------------------------------------------------gtatgtcctatcttcaagtgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG
||| | || | || | | || | || | | | || || | || ||| | | || | |||| || | |||| ||||| ||||||||||| || |||||||| ||||| |||||||||||||| || ||||| || ||||| |||||||| || ||||| ||
gtaagttcttaccttcctaaactgtttgtattagatcgcaaatttctactatactacttgttgaggtataatcataagcttgacctccatcaattttctttacaagtctctgattcatgttc---tatggtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------------------------------gtatgtcctatcttcaag-----tgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG
|| | | || || ||| | | | || | ||| || || | | || | | || | | ||| | ||||| || || ||||| ||||| || || ||||||||||| |||||||||||||| ||||||||||| |||||||| ||||| | || || ||
gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgatt----cagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG
upper sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S355_49V6.1 (Physcomitrella patens), 3'ss of exon 10
--------------------------------------------------------gtatgtcctatcttc-aagtgtttttc--------tatgatttgtttaaaagtagttgctatgacagat--------tctcagttatttatacatatgttc---attgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG
| |||| | | | | |||| || || | | | | | || | ||| | || | ||| ||| || | ||| | || ||| ||||||| || |||||||| |||||||||||| | ||||||||||||||||| || |||||||| || ||||| ||| |||| ||||| ||
gtatgcaattttacatttgccccgtgtttttatctttctaccaaactctcacctgagcatgttttgcttactgaacgtttctcgtttcacatagcaaaccatctatggcaagtgttttgaaatatcgaaatgttaatagtcgcttacacctgtgtcctaaatcacagAGAGAGTTTTACCTTGAAGGAGGTGCTATGGTTCTTGCTGATGGAGGTGTTGTCTGCATTGATGAGTTCGACAAAATGCGACCTGAAGACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG
ttatttatacatatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcctatcttcaagtgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA