Sequence
atgc intronic sequence ATGC exonic sequencegtaagatctttgaaattcaatattatgattaagattgttctccctcctaaatgtagctgttagtaaaatgaatcttcatgtgatgtaacttgcagGTTTGGAAGCTTACTTGCTTGTGAAAGCTTCCATGCTGATGTACATGCAGGAAACTTATGGCTGTTGCGTGATGGCCGGATTGGGTTTCTTGATTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G05200.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G05200.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os07g12530.2 (Oryza sativa), 3'ss of exon 8
---------gtaagatctttgaaattca-atattatg-attaagattgttctccctccta------aatgtagctgttagta-aaatgaatcttcatgtg-atgtaacttgcagGTTTGGAAGCTTACTTGCTTGTGAAAGCTTCCATGCTGATGTACATGCAGGAAACTTATGGCTGTTGCGTGATGGCCGGATTGGGTTTCTTGATTTTG
| | ||| | | || | || || ||| | | |||| || | || | | || | | | ||| || || ||||||||||||||||| || | |||||| ||||||||| ||||| ||||||||||| |||||| || | || ||||| || |||| |||||||||||||
gtatgctccatgcgtccttgtgattccatacatcatatatttgggtatttctgccattcattgccttattcaatcctcagaataggcatgttgacatatgtgcaaaatgtgcagGTTTGGAAGCTTGATTTCATGTGAATCCTTCCATGCAGATGTGCATGCAGGAAATTTATGGTTGCTCCGAGATGGACGTGTTGGATTTCTTGATTTTG
upper sequence: AT5G05200.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G031780_T02 (Zea mays), 3'ss of exon 5
------------------gtaagatctt-tgaaattcaatattatgattaagattgttctccctcc-taaatgtagctgttagtaaaatgaatcttc----atgtgatgtaacttgcagGTTTGGAAGCTTACTTGCTTGTGAAAGCTTCCATGCTGATGTACATGCAGGAAACTTATGGCTGTTGCGTGATGGCCGGATTGGGTTTCTTGATTTTG
||||| | || || |||| | | || || || ||| | | ||| | | | | | | |||| | || || || |||||||||||||||| || | |||||| ||||||||||||||||||||| |||||| ||||| || | |||||||| || ||||| ||| |||||||||
gtaagttgcactgctgtcacttcatcttgtatgatacaccatta--actgagttttttttcctttcataacctttgtagagcctttgttttaacttctgaaaaatgcaaaaaattacagGTTTGGAAGCTTAATTTCATGTGAATCCTTCCATGCTGATGTACATGCTGGAAACCTATGGTTGCTCCGTGATGGGCGAATTGGTTTTATTGATTTTG
upper sequence: AT5G05200.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G36520.1 (Glycine max), 3'ss of exon 6
gtaagatctttgaaattcaatattatgattaagattgttctccctcctaaatgtagctgttagtaaaatgaatcttcatgtgatgtaacttgcagGTTTGGAAGCTTACTTGCTTGTGAAAGCTTCCATGCTGATGTACATGCAGGAAACTTATGGCTGTTGCGTGATGGCCGGATTGGGTTTCTTGATTTTG
||| || || |||||| || || |||| || || | | | || | || | || |||| | | | | ||||||||||||||| || ||||| |||||| || ||||| ||||||||||||||||| | ||||| | ||||||||||| |||||||||||||| || |
gtatga-ctccgaaattatattttgcagttaacatcctttacttctcct--tttaaca---agaactgtgtatctcggtataaaatg--ttgcagGTTTGGAAGTTTGCTTGCATGTGAATCTTTTCATGCAGATGTACATGCAGGAAATCTGTGGCTTCTACGTGATGGCCGTATTGGGTTTCTTGACTTCG
upper sequence: AT5G05200.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv13s0067g03210.t01 (Vitis vinifera), 3'ss of exon 7
-------------------gtaagatctttgaaattcaatattatgattaagattgttctccctcctaaatgtagctgttagtaaaatgaatcttcatgt-gatgtaact-tgcagGTTTGGAAGCTTACTTGCTTGTGAAAGCTTCCATGCTGATGTACATGCAGGAAACTTATGGCTGTTGCGTGATGGCCGGATTGGGTTTCTTGATTTTG
| | | | || | || ||||| ||| | | || ||| || | ||| | ||||| | ||| | | ||||||||||| || || ||||| ||||||| ||| ||||| ||||| |||||||| || || ||| || | ||||||||||| |||||||||||||||||||
gtaggactcaaacttggatctgcagttcataagctttcttgttttgatttttatt-tattggctaataacatcagaatcttataagttcaatctcttcattgatatgtttctgcagGTTTGGTAGTTTGCTTGCCTGTGAAACCTTTCATGCAGATGTTCATGCAGGCAATTTGTGGTTGCTACGTGATGGCCGCATTGGGTTTCTTGATTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccctcctaaatgtagctgttagtaaaatgaatcttcatgtgatgtaacttgcagGTTTGGAAGCTTACTTGCTTGTGAAAGCTTCCATGCTGATGTACATGCAGGAAACTTATGGCTGTTGCGTGATGGCCGGATTGGGTTTCTTGATTTTG
ttagtaaaatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatctttgaaattcaatattatgattaagattgttctccctcctaaatgtagctgttagtaaaatgaatcttcatgtgatgtaacttgcagGTTTGGAAGCTTACTTGCTTGTGAAAGCTTCCATGCTGATGTACATGCAGGAAACTTATGGCTGTTGCGTGATGGCCGGATTGGGTTTCTTGATTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT