Sequence
atgc intronic sequence ATGC exonic sequence...tatttctaagaggtttatcatggatagttgacttaattgttcctaacagttctctggcttagtgtgcaacctcctaactttttaatgtgttttgatatagGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22770.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 3'ss of exon 8
----------------------------------------------------------------------tatttctaagaggtttat-catggatagttgacttaattgttcctaacagttc---tctggcttagtgtgcaacctcctaactttttaatgtgtttt--------------gatatagGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
| | | ||||| | | || ||| || || | | ||| |||| || | | | | | |||| || || ||||||| ||||||||||||||||| ||||| |||||||| ||||| || ||||||||||| ||||||||| | || || || || || || || ||||| ||
gtgagttcaaacgaaaacttctactactatatattttaatttctagcaatttgtttctcaaccagttcctcaccttccctacttttatattcatacaattatcttcatggtctccagtgtttcaccactggagtaaaataaagcttatcacgcatttagaatgcttctctaagttctcccgattatagGTTATGCATCTTGATGCTGAAAAGGAGATGATGTCCCAGTGCGTGGCTCTTCTTGGGAAGTTTATTGCAGTTCGGGAACCAAATATTAGGTATCTTGGTC
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 8
-----------------------------------tatttctaagaggtttatcatgga-tagttgacttaa--ttgttcctaacagttctctggcttagtgtgcaacctcctaact-------ttttaatgtgt----tttgatatagGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
| | | | ||| | | | | ||| || | | | || | || || | | || ||| | ||| |||| | | ||||||||||||||||| |||||||||||||| ||||||||||||||||| ||||||||||| ||||||||| | ||||| ||||| ||||| | || || ||
gtgagtttgtattgactttaaagcgattaatcccccaccctggtccgatcttgcattgccttttctgcataagtttatgcttcgcaaaatcacagtttggtatcctgtctattaattaagtctgtttgcatgtataatactccatatagGTCATGCATCTGGATGCTGAGAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTCGGTC
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G137236_T01 (Zea mays), 3'ss of exon 9
tatttctaagaggtttatcatggatagttgacttaattgttcctaacagttctctggcttagtgtgcaacctcctaactttttaatgtgttttgatatagGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
|||| | | || || | |||| | || || ||| | || | | ||||| || ||||||||||||||||| |||||||| ||||| ||||||||||||||||| ||||||||||| ||||||||| | ||||| ||||| ||||| | || || ||
--------gtgagtttgt-acttatgtttcgcaaaattacagtt--tggtatattgtctttttaattaagtctttgcacgtataatgc---ttcatatagGTCATGCATCTGGATGCTGAAAAGGAGATGATGTCACAGTGTGTGGCTCTTCTTGGGAAGTTTATTGCAGTCCGGGAGCCAAACATTCGGTACCTTGGTC
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 8
-----tatttctaagaggtttatcatggatagttgactta--attgttcctaacagttctctggcttagtgtgcaacctcctaactttttaatgtgttttgatatagGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
| | || || || | || ||| || || ||| | || |||| | | ||| || || | | || |||| ||||||||||||||||| || || |||||||| |||||||| ||||||||||| || |||||| |||||||||| || ||||| ||||||| ||||
gttaatctctccctcccccttctcccaatttacatacaggggattttttctcacaatgagatgttgtagt-tatactctctattctgattgctatattc------agGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAGTGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 8
tatttctaagaggtttatcatggatagttgacttaattgttcctaacagttctctggcttagtgtgcaacctcctaactttttaatgtg-ttttgatat--agGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
||| | || || || | | | ||| | || || | | ||| | || | || || |||| |||| ||||||||||||||||| || || |||||||| || ||||| ||||||||||| || |||||| |||||||||| || ||||| ||||||| ||||
-attctctccctccccccttctcccaatttacatacaagggatttttt-tcctcacaatcag-atgtagcagttatactctctattctgattgctatattcagGTGATGCATCTTGATGCTGAAAAAGAGATGATGTCTCAATGTGTGGCTCTTCTTGGAAAATTTATTGCTGTCCGTGAACCAAACATTCGATATCTTGGCT
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 8
-----tatttctaagaggtttatcatggatagttgacttaattgttcctaacagttctctggcttagtgtgcaacctcctaactttttaatgtgttttgatatagGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
|||| || | ||| | || | || | ||| || || | || || | | | | || | | || | ||||||||||||| |||||||| || ||||||||||| || |||||||| | ||||| || |||||| |||| || ||||| || || ||||||| || |
gttgggttttcctcttatttcaatgtgggt--ttaagatactggtttttatgagaattaagg---agcttttatgtggttgtgtccttcaattaccctggcacagGTCATGCATCTGGATGCTGAAAAAGAAATGATGTCTCAATGTGTTGCCTTGCTTGGGAAATTTATTGCTGTACGAGAGCCAAATATACGATATCTTGGTT
upper sequence: AT5G22770.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ34224 (Selaginella moellendorffii), 3'ss of exon 8
tatttctaagaggtttatcatggatagttgacttaattgttcctaacagttctctggcttagt-gtgcaacctcctaactttttaatgtgttttgatatagGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
|| || ||| | || || | | | | |||| | || | |||| |||||| | || || ||||| || |||||| |||| ||||||| ||| ||||| ||||||||| ||||||||||||||||||| ||||||| ||
------------------------------------------gtaggttttttctttttctgttgttccattcaagagcctttt----ttttgtcgcgcagGTGATGCATTTAGACGCAGAGAAAGATATGATGGCACAATGTGTTGGTCTACTTGGAAAGTTTATTGCTGTCCGTGAGCCCAACATTCGATATCTTGGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acagttctctggcttagtgtgcaacctcctaactttttaatgtgttttgatatagGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
tttttaatgtgttttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatttctaagaggtttatcatggatagttgacttaattgttcctaacagttctctggcttagtgtgcaacctcctaactttttaatgtgttttgatatagGTCATGCATCTTGATGCTGAGAAGGAAATGATGTCACAGTGTGTTGCTCTTCTTGGCAAGTTTATTTCTGTCCGTGAGCCCAACATCAGATATCTAGGCT
- - - - - -ggtttat
- - - - - - - - - - - - - - - - - - - - -cctaaca
- - - - - - - - - - - - - - - - - - - - - - - - -ttctctg