Sequence
atgc intronic sequence ATGC exonic sequencegtagaaaaaagtttttcttaaatgactcctctgagcatcaagttcctttttgtgaaaatagactttcttatgtcttcttttccttgtgctttaatattcatgaacagCCTGTCATACTTGATTACCTAGCAAGTAAGGCCATATCCTCTGAAGATTTGGTGGTAGTTTCACCTGATGTTGGTGGCGTCGCAAGAGCTCGCGCTTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G44530.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G44530.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S123_105V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------gtagaaaaaagtttttcttaaatgactcctctgagcatcaagttcctttt-tgtgaaaatagactttcttatgtcttcttttcc---ttgtgctttaata-------ttcatgaacagCCTGTCATACTTGATTACCTAGCAAGTAAGGCCATATCCTCTGAAGATTTGGTGGTAGTTTCACCTGATGTTGGTGGCGTCGCAAGAGCTCGCGCTTTTG
|| | ||||| | | | | | | | | || |||| ||| || | | ||| |||| || |||| || | | |||| | | ||||| || |||||||||||||| ||||||||| ||||| || | || ||||||||||| ||||| ||||||||||| || || | ||||| || ||||
gtgagcattttaacaagttttattattttattatttttaaaatttaaattttaaaattattgttattcttatttttttgttattctccctcaagtgtaacatgttctatttgtgctcggaggaaaattcacatgttttattttaaaggttattgtctaattgggaaaccttgtatgcagCCCGTAATACTTGATTACCTGGCAAGTAAGATGATATCGTCAAACGACTTGGTGGTAGTGTCACCAGATGTTGGTGGAGTTGCTCGTGCTCGTGCATTTG
upper sequence: AT2G44530.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ24123 (Selaginella moellendorffii), 3'ss of exon 4
gtagaaaaaagtttttcttaaatgactcctctgagcatcaagttcctttttgtgaaaatagactttcttatgtcttcttttccttgtgctttaatattcatgaacagCCTGTCATACTTGATTACCTAGCAAGTAAGGCCATATCCTCTGAAGATTTGGTGGTAGTTTCACCTGATGTTGGTGGCGTCGCAAGAGCTCGCGCTTTTG
| || || ||| || | | | | | | | ||| ||| || |||| | ||| || ||||||||||| | || ||||| || || || || ||| | || || || || |||||||| || ||||||||||| |||||||||||||| || ||||
----------------------------gtatgtgcgtcatatttttctcaacgtcacca--ttcccgtataaaatctctt-----tgctct----ttcttg--cagCCTGTCATTTTGGACTACCTTGCCAGCAAAATGATCTCCGCAGATGACTTAGTAGTAGTTTCTCCAGATGTTGGTGGTGTCGCAAGAGCTCGGGCATTTG
upper sequence: AT2G44530.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ35181 (Selaginella moellendorffii), 3'ss of exon 4
gtagaaaaaagtttttcttaaatgactcctctgagcatcaagttcctttttgtgaaaatagactttcttatgtcttcttttccttgtgctttaatattcatgaacagCCTGTCATACTTGATTACCTAGCAAGTAAGGCCATATCCTCTGAAGATTTGGTGGTAGTTTCACCTGATGTTGGTGGCGTCGCAAGAGCTCGCGCTTTTG
| || || ||| || ||| | || | | ||| | | || ||| |||| | ||||||||||| | || ||||| || || || || ||| | || || || || |||||||| || ||||||||||| |||||||||||||| || ||||
----------------------------gtatgtgcgtcatatt----tttctcaacgtcaccattcccgtacaaaaatctctttgctctttctt--------gcagCCTGTCATTTTGGACTACCTTGCCAGCAAAATGATCTCCGCAGATGACTTAGTAGTAGTTTCTCCAGATGTTGGTGGTGTCGCAAGAGCTCGGGCATTTGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|125232160|gb|EL246245.1|EL246245EST: CTACTTTGATATTCCAGTCGATCATGTTTATGGCCAG CCTGTCATACTTGATTACCTAGCAAGTAAGGCCATATCCTCTGAAGATTTG
genomic: CTACTTTGATATTCCAGTCGATCATGTTTATGGCCAGgtagaaaaaa ... tcatgaacagCCTGTCATACTTGATTACCTAGCAAGTAAGGCCATATCCTCTGAAGATTTG
EST:
gi|125259031|gb|EL273116.1|EL273116EST: GACAGTCTATGGGCTACTTTGATATTCCAGTCGATCATGTTTATGGCCAG CCTGTCATACTTGATT
genomic: GACAGTCTATGGGCTACTTTGATATTCCAGTCGATCATGTTTATGGCCAGgtagaaaaaa ... tcatgaacagCCTGTCATACTTGATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaaaatagactttcttatgtcttcttttccttgtgctttaatattcatgaacagCCTGTCATACTTGATTACCTAGCAAGTAAGGCCATATCCTCTGAAGATTTGGTGGTAGTTTCACCTGATGTTGGTGGCGTCGCAAGAGCTCGCGCTTTTG
ctttaat putative branch site (score: 4)
tttaatattcatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagaaaaaagtttttcttaaatgactcctctgagcatcaagttcctttttgtgaaaatagactttcttatgtcttcttttccttgtgctttaatattcatgaacagCCTGTCATACTTGATTACCTAGCAAGTAAGGCCATATCCTCTGAAGATTTGGTGGTAGTTTCACCTGATGTTGGTGGCGTCGCAAGAGCTCGCGCTTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT