Sequence
atgc intronic sequence ATGC exonic sequencegtttttgtttaccattctcttacctgcttgttatatttcaattctgttatccaatctgcttaacctggaaatttatcaaatttatacagCCAGACCTGACTGTGAGGGAGAAGATACTTAGTTTATTAGATACATGGCAAGAAGCTTTTGGTGGAAGCGGCGGAAGATTCCCTCAGTACTACAATGCCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G21380.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G21380.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G42250.1 (Glycine max), 3'ss of exon 4
------------------------------gtttttgtttaccattctcttacctgcttgttatatttcaa--ttctgttatccaat-ctgcttaacctggaaatttatcaaatttatacagCCAGACCTGACTGTGAGGGAGAAGATACTTAGTTTATTAGATACATGGCAAGAAGCTTTTGGTGGAAGCGGCGGAAGATTCCCTCAGTACTACAATGCCT
||||| | | |||| | || || | | | || | | ||||||| | |||||| || |||| | || ||||||| || | | ||||||||| |||||||| | |||| | ||||||||||||||||||||||| || ||| | ||||| ||||| || |
gtatttatttgttttgacactctatatttcatttttaatcttccttctgtaactgtattttggaaatggaagactttcttatccattgctgctt--tct-----tttaatgtaattgtacagCCGGATTTAAATGTGAGGGAAAAGATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGGGCCAACTGGAGTTTATCCTCAATACTATGCAGCAT
upper sequence: AT1G21380.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G12570.1 (Glycine max), 3'ss of exon 4
-----------------------gtttttgtttaccattctcttacctgcttgttatatttcaattctg----ttatccaatctgcttaacctggaaatttatcaaatttatacagCCAGACCTGACTGTGAGGGAGAAGATACTTAGTTTATTAGATACATGGCAAGAAGCTTTTGGTGGAAGCGGCGGAAGATTCCCTCAGTACTACAATGCCT---
| ||| || | ||| ||| | | ||||| | | | || ||| | | || ||| ||| ||||||| || | | ||||||||| || ||||| | |||| | ||||||||||||||||||||||| || | ||| | ||||| ||||| || |
gtatttattggttttgccactttatatttcatttttaatcttccttctg-taactgtatttggaagtggaagactttcttatccattgctgccttcttttgatctgatt-gtacagCCGGATTTAAATGTGAGGGAAAAAATACTGATTTTAATTGATACATGGCAAGAAGCTTTTGGGGG---CTATGGAGTTTATCCTCAATACTATGCAGCATATA
upper sequence: AT1G21380.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g01180.t01 (Vitis vinifera), 3'ss of exon 3
------------gtttttgtttacc--attctcttacctgcttgttata---tttcaattctgttatccaatctgcttaacctggaaatttatcaaatttatacagCCAGACCTGACTGTGAGGGAGAAGATACTTAGTTTATTAGATACATGGCAAGAAGCTTTTGGTGGAAGCGGCGGAAGATTCCCTCAGTACTACAATGCCT
| | | || || || | | | || | | || || || || | ||| | | |||||| | ||||||||| ||| ||| ||||| ||||| || | ||| ||||||| ||||||||||||||||| ||| | ||||||| || || ||||| ||| |
gtgcctaatttcatcctggcttgttttatgtatatatatatatatcatggcttgttgttttcattctcatattagtttatttttatctatgttcaaatct--gcagCCAGACTTGAATGTAAGGGAAAAGATTCTAATTTTGATAGATACGTGGCAAGAAGCTTTTGGGGGACCTAGGGGAAGATATCCCCAATACTATGCTGCATMapped 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|86072584|gb|DR368341.1|DR368341EST: TTGTTGACCGAGATATTTTACCTGATATGGTCAAAATAGTGAAGAAGAAG CCAGACCTGACT
genomic: TTGTTGACCGAGATATTTTACCTGATATGGTCAAAATAGTGAAGAAGAAGgtttttgttt ... atttatacagCCAGACCTGACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcaattctgttatccaatctgcttaacctggaaatttatcaaatttatacagCCAGACCTGACTGTGAGGGAGAAGATACTTAGTTTATTAGATACATGGCAAGAAGCTTTTGGTGGAAGCGGCGGAAGATTCCCTCAGTACTACAATGCCT
gcttaac putative branch site (score: 3)
aaatttatcaaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttgtttaccattctcttacctgcttgttatatttcaattctgttatccaatctgcttaacctggaaatttatcaaatttatacagCCAGACCTGACTGTGAGGGAGAAGATACTTAGTTTATTAGATACATGGCAAGAAGCTTTTGGTGGAAGCGGCGGAAGATTCCCTCAGTACTACAATGCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA