Sequence
atgc intronic sequence ATGC exonic sequence...tattttgtgttgaatgtttatggatgggtgatataatctgaagcgcatactttttgtgtccattcttactgatggtccagtctttttgctttttgtgtagTCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G38710.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G38710.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G24340.1 (Glycine max), 3'ss of exon 1
-----tattttgtgttgaatgtttatggatgggtgatataatctgaagcgcatactttttgtg-tccattcttactgatggtccagtctttttgctttttgtgtagTCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTC
| | | || || || | ||| ||| || | | | | | | | || | || || | || ||| | | |||||||||||||||||| ||||||||| | |||||||||||||| ||||| | || ||||||||||| || |||||||||||| ||||||||| ||| ||
agggggaaatccttttagcagtaaataaaaaaactatac---ttgagtcgacaatatgatataatatggtgtccttgtt--tcaagcaactatgttttgttt-tagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGCCTTCGGGGATGTATTGGAACTCTGGAAGCACGCAGCTTGATCAATGGGCTC
upper sequence: AT2G38710.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G18290.1 (Glycine max), 3'ss of exon 1
tattttgtgttgaatgtttatggatgggtgata----taatctgaagcgcatactttttgtgtccattcttactgatggtccagtctttttgctttttgtgtagTCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTC
| | | ||| || | | | ||| || || || | | | | | | | || || | | | |||| | |||||||||||||||||| ||||||||| | |||||||||||||| ||||| | || || || || || || |||||||||||| ||||||||| ||| ||
---taagggggaaatccttttagcggaaaaataagtctatacttgagtcgacaatatg-atataatatggtatccttgtttgaagcaacgatgttttgttttagTCCATTGTTTGTTACATGGAAGAAAGTGGTGAATGGTGGAGATCCTCGTCTTCGGGGTTGCATCGGAACTCTGGAAGCACGCAGCTTGATCAATGGGCTC
upper sequence: AT2G38710.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 1
--tattttgtgttgaatgtttatgg-atgggtgatataatctgaagcgcatactttttgtgt-ccattcttactgatggtccagtctttttgctttttgtgtagTCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTC
|||| | | || | || | | | | || | || | | || ||| | || || ||| || || || || ||||||| |||||||||||| ||||||||||||| || ||||| ||||||||||||||||| || || ||||| || ||||||||| ||||||
cccatttaataccagtttttaacaacatcaaatgaacagctttatgctctccacattggcatgttatcattatt--tgacacaaataattttctggtttc--agCCCTCTGTTTGTGACCTGGAAGAAAGTAGTGAATGGTGGGGAACCTCGTTTGCGTGGATGTATTGGAACTCTTGAAGCTCGTTGCTTGATCAATGGCTTT
upper sequence: AT2G38710.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ07623 (Selaginella moellendorffii), 3'ss of exon 1
tattttgtgttgaatgtttatggatgggtgatataatctgaagcgcatactttttgtgtccattcttactga-tggtccagtctttttgctttttgtgtagTCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTC
| | | || | | || | | | | || | | | || || ||| |||| || || ||||||||| | |||||||||||||||||||| ||||| ||||| || || || |||||||| ||| ||||||||| |||||||
------------------------------------------gtaagtgttcttggcattgtttgccattctctctttcacgttccattttccccatgcagCCCACTGTTCGTGACTTGGAAGAAAGTTGTGAATGGTGGAGAGCCTCGCTTGCGAGGATGCATCGGGACGCTGGAAGCTCGCTGCTTGATCACTGGCTTC
upper sequence: AT2G38710.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ11024 (Selaginella moellendorffii), 3'ss of exon 1
tattttgtgttgaatgtttatggatgggtgatataatctgaagcgcatactttttgtgtccattcttactgatggtccagtctttttgctttttgtgtagTCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTC
| ||| || | ||||||| || | || | | | | || || ||| |||| || || ||||||||| | |||||||||||||||||||| ||||| ||||| || || || |||||||| ||| ||||||||| |||||||
------------------------------------gtaagtgttcatggcattgtttgccattctctct-----ttcacgttccattttctccatgcagCCCACTGTTCGTGACTTGGAAGAAAGTTGTGAATGGTGGAGAGCCTCGCTTGCGAGGATGCATCGGGACGCTGGAAGCTCGCTGCTTGATCACTGGCTTCMapped 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|301501251|gb|HO206791.1|HO206791EST: CACTACAACAATGAAGAGACTCCACCACCTGCCTTTGAAGAGGCCAATCA TCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTT
genomic: CACTACAACAATGAAGAGACTCCACCACCTGCCTTTGAAGAGGCCAATCAgtaagttttt ... ttttgtgtagTCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTT
EST:
gi|164070605|gb|ES109907.1|ES109907EST: TGAAGAGGCCAATCA TCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTT
genomic: TGAAGAGGCCAATCAgtaagttttt ... ttttgtgtagTCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTT
EST:
gi|124780501|gb|EH870444.1|EH870444EST: CACCACAACAATGAAGAGACTCCACCACCTGCCTTTGAAGAGGCCAATCA TCCATTGTTTGTTA
genomic: CACTACAACAATGAAGAGACTCCACCACCTGCCTTTGAAGAGGCCAATCAgtaagttttt ... ttttgtgtagTCCATTGTTTGTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catactttttgtgtccattcttactgatggtccagtctttttgctttttgtgtagTCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTC
tactgat putative branch site (score: 2)
tctttttgctttttgt putative PPT
tttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattttgtgttgaatgtttatggatgggtgatataatctgaagcgcatactttttgtgtccattcttactgatggtccagtctttttgctttttgtgtagTCCATTGTTTGTTACCTGGAAGAAAATAGTGAATGGTGGAGAGCCTCGGTTGCGTGGATGTATTGGTACACTGGAAGCACGCCGCTTGATCAGTGGCTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG