Sequence
atgc intronic sequence ATGC exonic sequencegtaatttccgatctctgaatatttagaaagctacaaactttcaatttggttctattgattattgttgaatcctttttattattgtttagGATAAAATCTTGCAATCTACTGGTAGAGGTCATGCGGTCACTGTTACTAACGATGGTGCTACTATTCTCAAGTCACTTCACATAGACAACCCTGCAGCTA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20890.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os05g48290.3 (Oryza sativa), 3'ss of exon 3
--------------------------------------------gtaatttccgatctctgaatatttagaaagctacaaactttcaatttggttct--attgattattgttgaat--cctttttattat---tgtttagGATAAAATCTTGCAATCTACTGGTAGAGGTCATGCGGTCACTGTTACTAACGATGGTGCTACTATTCTCAAGTCACTTCACATAGACAACCCTGCAGCTA
| || | | | |||| | || | || || || || | ||| | || || ||||| ||| | | | |||| || ||| | ||||| ||||| || || | || |||||||| || ||||||||||| ||||| ||||| ||||| || |||||||| || ||||
gtatgctcaaaaatctaaagcatcctggttttcttcatttatttgcaaactatcacccctgatattggctcaaattttaatctactcatcaagtgccaaatttgtaatcacataaccgcctttctatgttctatactcagGACAAGATCCTACAATCAACTGGCAGGGGACGCAGTGTGACTGTTACAAATGATGGTGCTACAATTCTGAAGTCTCTTCATATCGACAACCCAGCTGCTA
upper sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 2
--------------------------------gtaatttccgatctctgaatatttagaaagctacaaactttcaatt--tggttctattgattattgttgaatc-ctttttattat-tgtttagGATAAAATCTTGCAATCTACTGGTAGAGGTCATGCGGTCACTGTTACTAACGATGGTGCTACTATTCTCAAGTCACTTCACATAGACAACCCTGCAGCTA
| | ||| | | || || | |||| ||| || | | |||| ||| | | | |||| || | | | ||||| || ||| ||||||| ||||||||||| | | || |||||||| || ||||| ||||| ||| | |||||||||||||| ||||| ||||| || |
gtatgtttttgaaacatattgttcatgccttggaaccgtccactttacatgaatgatagcagttttttacttctcattgttgttattgttgaaaatttgcaagttgcatttttttgtgtatgtagGACAAGATCCTGCAATCAACTGGTAGAGGGCGTAATGTTACTGTTACAAATGATGGGGCTACCATTTTGAAGTCACTTCACATTGACAATCCTGCTGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaactttcaatttggttctattgattattgttgaatcctttttattattgtttagGATAAAATCTTGCAATCTACTGGTAGAGGTCATGCGGTCACTGTTACTAACGATGGTGCTACTATTCTCAAGTCACTTCACATAGACAACCCTGCAGCTA
tattgat putative branch site (score: 3)
tcctttttattatt putative PPT
aatcctttttattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatttccgatctctgaatatttagaaagctacaaactttcaatttggttctattgattattgttgaatcctttttattattgtttagGATAAAATCTTGCAATCTACTGGTAGAGGTCATGCGGTCACTGTTACTAACGATGGTGCTACTATTCTCAAGTCACTTCACATAGACAACCCTGCAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT