Sequence
atgc intronic sequence ATGC exonic sequencegtaagtagtcattgtccctatcctgagtgtacctaaatacttgtttctatttagttcaccctcctgatttgtcatatactaattttgtgatatacttttggttgttcagCATGCAACCCACACAATTGTGTTTTCACAGCTTCATATCAACGGAACCAACCAGGGGGTCCATGCCTTTATCGCCCAAATCAGGGATCAAGATGGCAGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G06290.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G06290.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G43840.1 (Glycine max), 3'ss of exon 3
gtaagtagtcatt-gtccctatcctgagtgtacctaa----atacttgtttctatttagttcaccctcctgatttgtcatatactaattttgtgatatact-tttggttgttcagCATGCAACCCACACAATTGTGTTTTCACAGCTTCATATCAACGGAACCAACCAGGGGGTCCATGCCTTTATCGCCCAAATCAGGGATCAAGATGGCAGCA
|||| | | || || | | | ||| || | || || | |||| | || | | || ||||| ||| || | || | || || ||||||||||||||||||| || || ||||||||||| |||| || |||| ||| || ||||| ||||| ||||| ||||||||||||||| |||||| | ||
gtaatgatttttttgtatacttgataattgtttaaaatcctagacatgataacatttt-tcaactgctccaactttgtatatattaaccttatattaacttgttcttttattcagCATGCAACCCACACTATAGTCTTTTCACAGCTCTATATAAATGGAAGCAATCAAGGGGTGCATGCATTTATTGCCCAAATCAGGGATTCAGATGGAAACA
upper sequence: AT1G06290.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA12G14060.1 (Glycine max), 3'ss of exon 3
----------------gtaagtagtcattgtcccta-tcctgagtgtacctaaat-acttgtttctatttagttcaccctcctgatttgtcatatactaattttgtgatatact-tttggttgttcagCATGCAACCCACACAATTGTGTTTTCACAGCTTCATATCAACGGAACCAACCAGGGGGTCCATGCCTTTATCGCCCAAATCAGGGATCAAGATGGCAGCA
| | | ||||| | |||| | | || || ||| |||| | || | | || ||||| ||| || | || | || || ||||||||||||| ||||| || || ||||||||||| |||| || |||| ||| || ||||| ||||| ||||| ||||||||||||||| |||||| | ||
gtaatgatttttttgtacacttgttaattgtttaaaatcctagacatgataagattgggtgcttccatttt-tcaactgcgccaactttgtatatattaaccttatattaacttgttcttttattcagCATGCAACGCACACTATAGTCTTTTCACAGCTCTATATAAATGGAAGCAATCAAGGGGTGCATGCATTTATTGCCCAAATCAGGGATTCAGATGGAAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaccctcctgatttgtcatatactaattttgtgatatacttttggttgttcagCATGCAACCCACACAATTGTGTTTTCACAGCTTCATATCAACGGAACCAACCAGGGGGTCCATGCCTTTATCGCCCAAATCAGGGATCAAGATGGCAGCA
tactaat putative branch site (score: 1)
atatactaattttgtg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtagtcattgtccctatcctgagtgtacctaaatacttgtttctatttagttcaccctcctgatttgtcatatactaattttgtgatatacttttggttgttcagCATGCAACCCACACAATTGTGTTTTCACAGCTTCATATCAACGGAACCAACCAGGGGGTCCATGCCTTTATCGCCCAAATCAGGGATCAAGATGGCAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG