Sequence
atgc intronic sequence ATGC exonic sequencegttctaatttttgtatacacttcatcagaagaatacttagcttctaatttatatttatttttccgctgcaattctttgttttcagGTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTATTGAGCCTTGCACCGTTGTGATGGATTTAGAGGGTACCGATGGGAGAGAGCGTGGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13870.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G01230.1 (Glycine max), 3'ss of exon 3
gttctaatttttgtatacacttcatcagaagaatact-tagcttctaattta--tatttatttttccgctgcaattctttgttttcagGTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTATTGAGCCTTGCACCGTTGTGATGGATTTAGAGGGTACCGATGGGAGAGAGCGTGGT
| |||| | || ||| | ||| | ||||||| || | || | | | || | | |||||||||||||||| || || || ||||| ||||| |||||||| ||||| || |||||||| || ||||||||||||| |||||||| ||||| ||||| || ||
-----gtatgttgt-tgcaattctgacatgttacactatcccttctaaactaactgggtaatgacctgatgtatatgcttgttttcagGTCTCAAACAACCAAAGGAATCTGGATGGCTAGATGTGCTGGCATAGAGCCTTGTACACTTGTGATGGATTTGGAGGGTACAGATGGAAGAGAACGCGGA
upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G02780.1 (Glycine max), 3'ss of exon 3
gttctaatttttgtatacacttcatcagaagaatacttagcttctaatttatatttatttttccgctgcaattctttgttttcagGTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTATTGAGCCTTGCACCGTTGTGATGGATTTAGAGGGTACCGATGGGAGAGAGCGTGGT
| ||| | |||| | | | | | ||||||||||||||||| || || | ||||||||||| |||||||| | ||| || |||||||| || ||||||||||||| |||||||| ||||| ||||| |||||
---------------------------gtccaatctggctatcacaattaacaaggtgaacctgataggacgtgtttgttttcagGTCTCAAACAACCAGAGGAATTTGGATGGCTAGATGTGTTGGGATAGAGCCTTGTACACTTGTGATGGATTTGGAGGGTACTGATGGAAGAGAACGTGGA
upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G20610.1 (Glycine max), 3'ss of exon 3
gttctaatttttgtatacacttcatcagaagaatacttagcttctaatttatatttatttttccgctgcaattctttgttttcagGTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTATTGAGCCTTGCACCGTTGTGATGGATTTAGAGGGTACCGATGGGAGAGAGCGTGGT
|| || | ||| | || || | |||| | | | || | || | | |||||||||||||||| || || || ||||| ||||| |||||||| |||| || |||||||| || ||||||||||||| |||||||| ||||| ||||| |||||
gtatgttgttgcaattctgacatgtcacacaaacctttctcaactaactggg---tggtgatctgatgtatatgcttgttttcagGTCTCAAACAACCAAAGGAATCTGGATGGCTAGATGTGCTGACATAGAGCCTTGTACACTTGTGATGGATTTGGAGGGTACAGATGGAAGAGAACGTGGA
upper sequence: AT3G13870.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G42650.1 (Glycine max), 3'ss of exon 4
gttctaatttttgtatacacttcatcagaagaatacttagcttctaatttatatttatttttccgctgcaat-tctttgttttcagGTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTATTGAGCCTTGCACCGTTGTGATGGATTTAGAGGGTACCGATGGGAGAGAGCGTGGT
| | | | || | |||||||||||||||| || || | ||||||||||| |||||||| | ||| || |||||||| || ||||||||||||| |||||||| ||||| ||||| |||||
--------------------------------------------------------gtgaacctgataggatgtgcttgttttcagGTCTCAAACAACCAGAGGAATTTGGATGGCTAGATGTGTTGGCATAGAGCCTTGTACACTTGTGATGGATTTGGAGGGTACTGATGGAAGAGAACGTGGAMapped 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|116444534|gb|EG487126.1|EG487126EST: ATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAA-G--- GTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTATTGAGCC
genomic: ATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGGCATgttctaattt ... ttgttttcagGTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTATTGAGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatacttagcttctaatttatatttatttttccgctgcaattctttgttttcagGTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTATTGAGCCTTGCACCGTTGTGATGGATTTAGAGGGTACCGATGGGAGAGAGCGTGGT
ttctaat putative branch site (score: 2)
ttctttgttttc putative PPT
ttagcttctaatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttctaatttttgtatacacttcatcagaagaatacttagcttctaatttatatttatttttccgctgcaattctttgttttcagGTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTATTGAGCCTTGCACCGTTGTGATGGATTTAGAGGGTACCGATGGGAGAGAGCGTGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA