Sequence
atgc intronic sequence ATGC exonic sequence...gcaaacctttgagttgcaatcaaataatttctcaaatcacagctactagtgtcccatgttcttgatatgttgacttagacgctcatttctttaactgcagAGCCGAGACAGATCAAATGGAAGTCAAGGGGGTCCAAGACAAAGGGCTGAAGCTTTAGCCGCCTTAACATCCGCATTCAATTCTTCACCATCATCAAAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G57410.1 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 20
gcaaacctttgagttgcaatcaaataatttctcaaatcacagctactagtgtcccatgttcttgatatgttgacttagacgctcatttctttaactgcagAGCCGAGACAGATCAAATGG---AAGTCAAGGGGGTCCAAGACAAAGGGCTGAAGCTTTAGCCGCCTTAACATCCGCATTCAATTCTTCA-CCATCATCAAAGT--
||| ||| | || ||| | || | || | | | | | | | | ||| | ||||| | || | || | || ||||| ||||| ||| || |||||||||||||||||||| ||||| ||||||| || ||||| ||||| ||| | | ||||||
-taaaattttaat-----atttaattgtgtcatagatgataattggataaaccaaacaaacaaattggttctcctttctaatttttttctactctgactgacacagGATAAGTCGAATGGGCTAAGTCGAGGAGGACCAAGACAAAGGGCTGAAGCCTTAGCAGCCTTAAACTCTGCATTTAATTCATCATCTGGAACCAAAGTTT
upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 20
gcaaacctttgagttgcaatcaaataatttctcaaat-cacagctactag--tgtcccatgttcttgatatgttga---cttagacgctcatttctttaactgcagAGCCGAGACAGATCAAATGG---AAGTCAAGGGGGTCCAAGACAAAGGGCTGAAGCTTTAGCCGCCTTAACATCCGCATTCAATTCTTCACCATCATCAAAGT
|| | | | || | | || | | | || ||| |||| | | ||| | | || | | ||| | ||||| | ||| |||| ||||| | | |||||||| ||||| |||||||| |||||||||||||| |||| || ||||| ||||| ||| | | |
------ctataaccttcattattgtttctttgtggttgtgttgtcattattctgttccattattctattataatcagttctcaattaaccctttgccttcttgcagGCACAAGATAGATTGAATGGGTTAGGCCAAGGGGGACCAAGGCAAAGGGCAGAAGCTTTAGCCGCTTTAAACTCTGCATTTAATTCATCATCTGGGACGA---
upper sequence: AT3G57410.1 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA02G32100.1 (Glycine max), 3'ss of exon 19
-gcaaacctttga-gttgcaatcaaataatttctcaaatcacagctactagtgtcccatgttcttgatatgttgacttagacgctcatttctttaactgcagAGCCGAGACAGATCAAATGG---AAGTCAAGGGGGTCCAAGACAAAGGGCTGAAGCTTTAGCCGCCTTAACATCCGCATTCAATTCTTCACCATCATCAAAGT
|||||| |||| | || ||| | || | || || || ||| | | ||| | ||||| | ||| |||| ||||| | | ||||| || |||||||||||||| |||||||||||||| |||| || ||||| | ||| ||| | | |
gtttaaccttcattattgcttctttgtggttgtgttg-tcattatt-ctgttccattattcaattatcatcaatactcaattaaccctttgccttcttgcagGCACAAGATAGATTGAATGGGTTAGGCCAAGGAGGACCAAGACAAAGGGCAGAAGCTTTAGCCGCTTTAAACTCTGCATTTAGTTCATCATCTGGGACGA---Mapped 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|125037151|gb|EL109420.1|EL109420EST: CCTTGACTTCTGCCTTTAATTCTTCTTCTGGGAGAACAAGCTCTCCG AGCCGAGACAGATCAAATGGAAGTCAAGGGGGTCCAAGACAAAGGGCTGAA
genomic: CCTTGACTTCTGCCTTTAATTCTTCTTCTGGGAGAACAAGCTCTCCGgtaaatagtc ... ttaactgcagAGCCGAGACAGATCAAATGGAAGTCAAGGGGGTCCAAGACAAAGGGCTGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagtgtcccatgttcttgatatgttgacttagacgctcatttctttaactgcagAGCCGAGACAGATCAAATGGAAGTCAAGGGGGTCCAAGACAAAGGGCTGAAGCTTTAGCCGCCTTAACATCCGCATTCAATTCTTCACCATCATCAAAGT
ctttaac putative branch site (score: 3)
ctcatttcttt CT-rich tract
atttctttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaaacctttgagttgcaatcaaataatttctcaaatcacagctactagtgtcccatgttcttgatatgttgacttagacgctcatttctttaactgcagAGCCGAGACAGATCAAATGGAAGTCAAGGGGGTCCAAGACAAAGGGCTGAAGCTTTAGCCGCCTTAACATCCGCATTCAATTCTTCACCATCATCAAAGT
-caaacct
- - - - - - - - -aatcaaa
- - - - - - - - - - - - - - - - - aatcaca