Sequence
atgc intronic sequence ATGC exonic sequencegttagttctttctctcggttatgcgctcattagctcattgatcttgtttgagtagctaaggttttgtgaaaatgttcgtcttgtggtctgcagTTTATCCCGATGGCCGCGTTTGTATATCTATTCTACATCCTCCTGGTGATGATCCAAGTGGATATGAGCTTGCAAGTGAGCGTTGGACGCCTGTTCACAC
Basic information
| species | Arabidopsis thaliana |
| transcript | AT3G46460.1 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G46460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 1
gttagttctttctctcggttatgcgctcattagctcattgatcttgtttgagtagctaaggttttgtgaaaatgttcgtcttgtggtctgc-agTTTATCCCGATGGCCGCGTTTGTATATCTATTCTACATCCTCCTGGTGATGATCCAAGTGGATATGAGCTTGCAAGTGAGCGTTGGACGCCTGTTCACAC
|| | || || | |||| || | | | | | | | |||| | | | | || ||| ||||||||| ||||| || || || || |||||||| ||||| |||||||||||||| | ||| ||||||||||| |||||||||||||| || || || ||
----gtcagctttcctcattgtaacttcat------gtttctgtaactccatgatccataattttaacacagcataatattggtcaattgccagTTTATCCGGATGGACGTGTATGCATTTCTATTCTTCATCCGCCTGGTGATGATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATAC
upper sequence: AT3G46460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G007300_T02 (Zea mays), 3'ss of exon 3
gttagttctttctctcggttatgcgctcattagctcattgatcttgtttgagtagctaaggttttgtgaaaatgttcgtcttgtggtctgc-agTTTATCCCGATGGCCGCGTTTGTATATCTATTCTACATCCTCCTGGTGATGATCCAAGTGGATATGAGCTTGCAAGTGAGCGTTGGACGCCTGTTCACAC
|| || | ||| | | | | | | ||| | || ||| | | | | | | || | || | | | | ||| ||||||| | ||||| | || ||||| |||||||| ||||| |||||||| ||||||||||| |||||||| ||||||||||||||||| ||||| || ||
gtaagatttttat-tagtgaaagttgtatttatttagtttatccgctgttatgttttctgacatcatgcatat---tatttggggaaatgccagTTTATTCAGATGGGCTGGTGTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAGTGGTTATGAGCTCGCAAGTGAGCGTTGGACACCTGTGCATAC
upper sequence: AT3G46460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
gttagttctttctctcggttatgcgctcattagctca-ttgatctt--gtttgagtagctaaggttttgtgaaaatgttcgtcttgtggtctgcagTTTATCCCGATGGCCGCGTTTGTATATCTATTCTACATCCTCCTGGTGATGATCCAAGTGGATATGAGCTTGCAAGTGAGCGTTGGACGCCTGTTCACAC
|| || |||| | | || | ||| | | || |||| ||| | || | | || | ||| || | | | |||| ||||| ||||| || |||||||| |||||||| ||||| |||||||| ||||||| || |||||||| ||||||||||| ||||| ||||| |||||
gtcag--ctttttattagtgaaaattgtatttatttacttcatctgcagttctgttttctgacatcatgc-ataatatttga---ggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
upper sequence: AT3G46460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
gttagttctttctctcggttatgcgctcattagctcattgatcttgtttgagtagctaaggttttgtgaaaatgttcgtcttgtggtctgcagTTTATCCCGATGGCCGCGTTTGTATATCTATTCTACATCCTCCTGGTGATGATCCAAGTGGATATGAGCTTGCAAGTGAGCGTTGGACGCCTGTTCACAC
|| || | | | | | | | || ||||| ||| ||| | || | | || | ||| ||| |||||||||| ||||| || ||||| || |||||||| ||||| |||||||| ||||| ||||| |||||||||||||| || || ||||| || || |||||
gtaagcttcactatcggactgtactcatgtctactatctgatcatgtcaaagttctgacaattct-------tatt-attttgaattct-cagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC
upper sequence: AT3G46460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G012052_T01 (Zea mays), 3'ss of exon 3
gttagttctttctctcggttatgcgctcattagctcattgatcttgtttgagta-gctaaggttttgtgaaaa-tgttcgtcttgtggtctgcagTTTATCCCGATGGCCGCGTTTGTATATCTATTCTACATCCTCCTGGTGATGATCCAAGTGGATATGAGCTTGCAAGTGAGCGTTGGACGCCTGTTCACAC
|| |||| || | || | | | ||||| | || || ||| || || | || || ||| ||| |||||||||| ||||| || ||||| || |||||||| ||||| |||||||| ||||| | ||| |||||||||||||| || || ||||| || || |||||
--------------gtaagcat-cgct-atcatgtcttgtctactatttgatcatgccaaagttctgacaattctttttgttttgaattct-cagTTTATCCTGATGGACGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAATGGTTATGAGCTTGCAAGCGAACGATGGACACCAGTGCACAC
upper sequence: AT3G46460.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
gttagttctttctctcggtt----atgcgctcat-tagctcattgatcttgtttgagtagctaa--ggttttgtgaaaatgttcgtcttgtggtctgcagTTTATCCCGATGGCCGCGTTTGTATATCTATTCTACATCCTCCTGGTGATGATCCAAGTGGATATGAGCTTGCAAGTGAGCGTTGGACGCCTGTTCACAC
| || || | | | | |||| ||||| | || | | | | | || || || | ||| | | ||| | | |||||||||||| ||||| || ||||| || || ||||||||| |||||||||||||||||| ||| ||||| | || |||||||||||| | || || || ||
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatcttgtttgagtagctaaggttttgtgaaaatgttcgtcttgtggtctgcagTTTATCCCGATGGCCGCGTTTGTATATCTATTCTACATCCTCCTGGTGATGATCCAAGTGGATATGAGCTTGCAAGTGAGCGTTGGACGCCTGTTCACAC
cattgat putative branch site (score: 4)
aaaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttctttctctcggttatgcgctcattagctcattgatcttgtttgagtagctaaggttttgtgaaaatgttcgtcttgtggtctgcagTTTATCCCGATGGCCGCGTTTGTATATCTATTCTACATCCTCCTGGTGATGATCCAAGTGGATATGAGCTTGCAAGTGAGCGTTGGACGCCTGTTCACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
