Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G04170.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g41400.1 (Oryza sativa), 3'ss of exon 3
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
|| | | | | |||| || | ||| | | || | | | ||| || || | | | || || |||||| | | | ||||||||||| || || || ||||| ||||||||||||| || || |||||||| ||||| || || || || ||||||||||| || ||||||||||| |||
----------gttgt-tgaactgctcaatcgt--ttttagta-tgtatgtacttcata---tgcaatctgtttatttgttttatatagttctgatttcttccttgtgattt--gtacagACTGTTCGCTTCAAGAATGAGCTGGAGCGTAACATCACTATAAAGCTTGGTTATGCTAATGCGAAAATCTACAAATGTGAAGACGAGAAATGCCCACGAC
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g07740.1 (Oryza sativa), 3'ss of exon 3
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
| | ||| | | || | || | | | || | | || | || || ||| | || ||| | ||| |||||| | | | | |||| || || || || ||||| ||||||||||||| || || |||||||| ||||| || || || || ||||||||||| || |||||||| || |||
---------gttcatgaacatctttcatatttagtatttatg---ttcttcacatgtaa---ttcatatatttatatttgtatagttgtcctgatgtcttccttgtgatttgt----agACCGTTCGCTTCAAGAATGAGCTGGAGCGTAACATCACTATAAAGCTTGGCTATGCTAATGCGAAAATCTACAAATGTGAAGACGAGAAATGTCCACGAC
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G18240.2 (Glycine max), 3'ss of exon 3
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
|| || | || || || || || || || | ||| ||| || ||| | || | || ||| | | | |||||| | | | || |||||||| ||||| |||||||| ||||||||||||||||| || |||||||| |||||||| || || || ||||| ||||| ||||| ||| || || |
-------ttatacataagcattccatcttt-tattcttaatacacatttt--cttttagctttggat-atttacactgt------tgacctgtgttgtttccgtgaatgtt--gtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCAAATGCAAAAATATACAAGTGTGAAGATGAACGATGTCCAAGGC
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G40750.1 (Glycine max), 3'ss of exon 3
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatt-tctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
|| ||| | | || || | || | | | | | | | || || | || || | | | || ||| |||||||| ||||| |||||||| ||||||||||||||||| || |||||||| ||||| || || || || ||||| ||||| ||||| || || || |
--------------------ttacacgtaagcatgccatatattattcttcatacacattctccgttagccttggatatttaaactgttgacctctgttgttttcatgaatgttgtgcagACTGTGCGTTTCAAAAATGAGTTGGAGCGTAACATTACAATCAAGCTTGGCTATGCTAATGCAAAAATATACAAGTGTGAAGATGAACGGTGTCCAAGGC
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0074g00310.t01 (Vitis vinifera), 3'ss of exon 3
gtaaaatttgattatgcggttttc-acaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
||| | | | || || || ||||| || || | | | | | | | || || | | | |||| ||| |||||| ||||||||| |||||||||||||| ||||||| || ||||| || || |||||||||||||| || ||||| ||||||||||| ||||| |||||| | |
-----------ttaggagacagtggaccatagtcatcctctag--ttattttgttaagaatatctatatgcttagatctgaaaggtggccctttatgatttgtttatct-------acagACTGTTCGTTTTAAAAATGAGCTGGAGCGAAATATTACTATCAAACTTGGATATGCAAATGCAAAGATATACAAATGTGAAGATGAACGGTGCCCTCGTC
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0042g01220.t01 (Vitis vinifera), 3'ss of exon 2
gtaaaatttgattatgcggtt-ttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggag-tgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
|| | | || || || |||||||| | || | | | | ||| || | || | | | | |||||||| |||||| ||||||||| |||||||||||||| ||||||| |||||||| || || |||||||||||||| |||||||| ||||||||||| ||||| |||||| |||
------------tagaagatggttgaccatagtaatcctctaa--ttactttgttaaaaatatttacaggcttaaatctgaaaggtgggtcctttatggtttatttatct-------acagACTGTTCGTTTTAAAAATGAGCTGGAGCGCAACATTACTATCAAACTTGGATATGCAAATGCCAAGATATACAAATGTGAAGATGAACGGTGCCCTCGAC
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ14781 (Selaginella moellendorffii), 3'ss of exon 1
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaat-tggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
| | | |||||| || | || | |||| | || || | | | | | ||| | || ||||||||||| || || |||||||||||||||||||| || || ||||| || ||||| || || |||||||||| ||||| || ||| ||||||| | |
-----------------------------------------gtgatctagagcttgttttgtgtctccagtgccgagttgatgttgttttctttgtttgattctttgttctgcttctcagACTGTCCGCTTCAAGAATGAATTGGAGCGTAACATCACAATCAAGCTCGGCTATGCGAATGCGAAGATTTACATGTGTGAAGACGAGCGATGCCCTCGGC
upper sequence: AT1G04170.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ26525 (Selaginella moellendorffii), 3'ss of exon 1
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttcta-gcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
|| ||| ||||| | || | | | ||| | | ||| || | | | ||| | || || | ||| || ||||||||||| || || |||||||||||||||||||| || || ||||| || ||||| || || |||||||||| ||||| |||||| ||||||| | |
------------------------------gtgatc-tagagcttgttttgtgtctccagtgccgagt---ttgatgttgtt----ttctttgtttgattctttgttctgcttc--tcagACTGTCCGCTTCAAGAATGAATTGGAGCGTAACATCACAATCAAGCTCGGCTATGCGAATGCGAAGATTTACATGTGTGAAGATGAGCGATGCCCTCGGCMapped 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|164146805|gb|ES184847.1|ES184847EST: ATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAG ACTGTACCGTTT-AAAAATGAATTGGAGCGTAACATTACCATTAAG
genomic: ATGTCGCTCATGGAAAGTCCACTGTTGTTAAAGCTATTTCTGGTGTCCAGgtaaaatttg ... ctctgtacagACTGT-CCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
gtttgat putative branch site (score: 5)
tttccttatcttctct putative PPT
atttctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatttgattatgcggttttcacaattgtaatcctagaggcttttctagcttgcagcgtttgatcaattggagtgggtgaagtgatttctatggtttccttatcttctctgtacagACTGTCCGTTTTAAAAATGAATTGGAGCGTAACATTACCATTAAGCTTGGATATGCAAACGCCAAGATTTACAAATGTGAGGATGAGAAATGCCCTAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG