Sequence
atgc intronic sequence ATGC exonic sequencegtacttgtttatgaccttcgtaggagatctttcatattgagttgtttgttcactcgttacatgtttaatgtagGTTGGATCAGGGAATACTGATGATGGAAATACAGATCCTAATGACCATTACTGTTGGATGCGACCTGAGGATATGGACTATAAAAGGCCCGTGACTACTT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G49720.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G110735_T01 (Zea mays), 3'ss of exon 2
---------------------------gtacttgtttatgaccttcgtaggagatctttcatattgagttgtttgttcactcgttaca-----------tgtttaatgtagGTTGGATCAGGGAATACTGATGATGGAAATACAGATCCTAATGACCATTACTGTTGGATGCGACCTGAGGATATGGACTATAAAAGGCCCGTGACTACTT
| || || | || | || || |||| || |||| |||| | ||| || |||| || ||| | || | | || | | | ||||||||||||||||| |||||| |||| ||||| || ||||| |||||||| || || |
gttggtagccatagatcatcttgcttgatggctgatttgctctgtcccaagaaattggtcat-cagatccaccaaaccactgactacaacatgaacttctcgttattgcagGTGGGTGTAGGTGACACCTCTAAAGGCAGCAGTCAGCCTAATGACCATTACTGCTGGATGAGACCAGAGGACATCGACTACAAAAGGCCAGTCACCGAGT
upper sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0035g02180.t01 (Vitis vinifera), 3'ss of exon 2
------------gtacttgtttatgaccttcgtaggagatctttcatattgagttgt----ttgttcactcgt-tacatgtttaat----------gtagGTTGGATCAGGGAATACTGATGATGGAAATACAGATCCTAATGACCATTACTGTTGGATGCGACCTGAGGATATGGACTATAAAAGGCCCGTGACTACTT
|| | | || || |||| | | || || | |||| || | |||| || | |||||||| ||| ||||| | || | |||| ||| ||||||||||| ||||||||||| |||||||| || || |||||| | || || || |
actattgctaatgttttagctttggatcttctgaaaatgctcagtcagttagattatgcaattgtattctgatgtacacagttcctcctctttttgacagGTTGGAATAGGAGATACTTCCGGGGGGAGTACAACTCCCAATGACCATTATTGTTGGATGCGCCCTGAGGACATTGATTATAAACGTCCTGTAACAGAATMapped 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|125284716|gb|EL298801.1|EL298801EST: CTGCTGATTCCATTGATGATCTTGTGTCACAG GTTGGATCAGGGAATACTGATGATGGAAATACAGATCCTAATGACCATTAC
genomic: CTGCTGATTCCATTGATGATCTTGTGTCACAGgtacttgttt ... tttaatgtagGTTGGATCAGGGAATACTGATGATGGAAATACAGATCCTAATGACCATTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtaggagatctttcatattgagttgtttgttcactcgttacatgtttaatgtagGTTGGATCAGGGAATACTGATGATGGAAATACAGATCCTAATGACCATTACTGTTGGATGCGACCTGAGGATATGGACTATAAAAGGCCCGTGACTACTT
gtttaat putative branch site (score: 4)
tttcatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttgtttatgaccttcgtaggagatctttcatattgagttgtttgttcactcgttacatgtttaatgtagGTTGGATCAGGGAATACTGATGATGGAAATACAGATCCTAATGACCATTACTGTTGGATGCGACCTGAGGATATGGACTATAAAAGGCCCGTGACTACTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT