Sequence
atgc intronic sequence ATGC exonic sequencegtgtgttctcactctcttctcttatcaagtcttaatttttgcatgtggttttgtacttaactttttattaatattgttgacagAACTACACAAGAAGGAAACATGTGAAGCTGTGACGATCATTGAGACACCTCCAATGGTGGTTGTTGGTGTGGTTGGTTATGTAAAGACACCTCGTGGTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G61580.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 3'ss of exon 3
-------------------gtgtgttctcactctcttctcttatcaagtcttaatttttgcatgtggttttgtacttaactttttattaatattgttgacagAACTACACAAGAAGGAAACATGTGAAGCTGTGACGATCATTGAGACACCTCCAATGGTGGTTGTTGGTGTGGTTGGTTATGTAAAGACACCTCGTGGTCT
| | ||| | | | | | | || | | ||| ||| | |||| |||| | || ||||||| ||||||||||| || ||||| ||||| || || |||||||||||||| || || |||||||| | || | ||||| ||||| || ||||| |
tggcctttagccaagactttaatactaagactttagtattcatctgaatatgcatactactgaagagatttaaccttgtcatttttctaatgctttt--cagAACTCCACAAGAAGGAGACCTGTGAGGCTGTTACCATTATTGAGACACCTCCTATTGTCGTTGTTGGACTTGTGGCCTATGTGAAGACTCCACGTGGCTT
upper sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G361049_T01 (Zea mays), 3'ss of exon 9
gtgtgttctcactctcttctcttatcaagtcttaatttttgcatgtggttttgtacttaactttttattaatattgttgacagAACTACACAAGAAGGAAACATGTGAAGCTGTGACGATCATTGAGACACCTCCAATGGTGGTTGTTGGTGTGGTTGGTTATGTAAAGACACCTCGTGGTCT--------------------------------------------------------------------------------------
| || || |||| |||| || |||||||||||||| ||||| |||||||| ||||||||||| ||||| | || |||| || | || | |||| ||||| || ||||| ||
-----------------------------------------------------------------tgttgattttgt--gcagagctccacaagaaggaaacttgtgaggctgtgactatcattgagactcctccccttgtcattgtcggacttgtgga--atgtgaagACCCCCCGTGGCCTACGAACCCTCAACTCTGTCTGGGCCCAACACCTTAGCGAAGAAGTGCGGAGAAGGTTCTACAAGAACTGGTGCAAGAGCAAGAAGA
upper sequence: AT1G61580.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv12s0035g01020.t01 (Vitis vinifera), 3'ss of exon 2
---------gtgtgttct-cac-tctcttctcttatcaagtcttaatttttgcatgtggttttgtacttaactttttattaata------ttgttgacagAACTACACAAGAAGGAAACATGTGAAGCTGTGACGATCATTGAGACACCTCCAATGGTGGTTGTTGGTGTGGTTGGTTATGTAAAGACACCTCGTGGTCT
|||| | | ||| ||| |||| | | ||||||| ||| | || | | || || ||| | | ||||||||||||||||| |||||||| ||||| || || ||||| || || || |||||||||||||||||||| ||||||||| | |||||||| ||||| ||
ccaggaaaaatgtggtttgcacatctaaagcattattattttttaatttaattttgtcatgctgcatcactgtattcatgaatcactccctccctaacagAACTACACAAGAAAGAAACATGCGAAGCAGTAACTATCATAGAAACGCCACCAATGGTGGTTGTTGGTGTTGTTGGTTATCTCAAGACACCGCGTGGCCTMapped 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|19876135|gb|AU236966.1|AU236966EST: CAAAGCTGGGATGACTCACATTGTGAGAGATGTTGAAAAACCTGGATCAA AACTACACAAGAAGGAAACATGTGAAGCTGTGACGATCATTGAGACACCTC
genomic: CAAAGCTGGGATGACTCACATTGTGAGAGATGTTGAAAAACCTGGATCAAgtgtgttctc ... ttgttgacagAACTACACAAGAAGGAAACATGTGAAGCTGTGACGATCATTGAGACACCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcttaatttttgcatgtggttttgtacttaactttttattaatattgttgacagAACTACACAAGAAGGAAACATGTGAAGCTGTGACGATCATTGAGACACCTCCAATGGTGGTTGTTGGTGTGGTTGGTTATGTAAAGACACCTCGTGGTCT
tattaat putative branch site (score: 2)
ttttgtacttaacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgttctcactctcttctcttatcaagtcttaatttttgcatgtggttttgtacttaactttttattaatattgttgacagAACTACACAAGAAGGAAACATGTGAAGCTGTGACGATCATTGAGACACCTCCAATGGTGGTTGTTGGTGTGGTTGGTTATGTAAAGACACCTCGTGGTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG