Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcattagaacttcatcctcttgtgtttgactccgatccatttaaaacatctctcgaataattcggtttcttgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G43945.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g23680.3 (Oryza sativa), 3'ss of exon 2
gtaagtcattagaacttcatcctcttgt-gtttgactccgatccatttaaaacatctctcgaat-aattcggtttct----tgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC
||| |||| ||| | || | | | ||| | || || | | ||| ||| ||| ||| | |||||||||||||||||| |||||| ||||| ||||| |||||||| || || ||| | ||||| || || || || | |||||| |||| || |||||| |||
gtatgtcac-agagtcttatggtataatagttcttccaatatttgattcatgtactactctaattaatattatttgttggctgcagAAAAATCATATATTCACATCTGGTGCTTCTGGGACTAATGCAGCTGTTATCCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTAC
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G022090_T02 (Zea mays), 3'ss of exon 1
-----------------------------gtaagtcattagaacttcatcctcttgtgtttgac----tccgatccatttaaaacatctctcg-aataattcggttt--cttgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC
| | || | || | ||||||| | || || || | ||| | ||| || || | ||||||||||||||||||| ||||| ||||| |||||||| ||||| || || ||||| ||||| | ||||| || | ||||||||||||||| |||||| |||
gtatgttcctatgtgctgttgtcatccatatgatctccctgatttatatgccagtgtgttttatatgatcttatatccttctagcattgttaataatgtttgtgtataatttgcagAAAAATCATATATTTACATCTGGTGCTTCTGGAACAAATGCAGCTGTTATCAGGGGTGCTCTAAGAGCTGAAAAACCAGAGCTGCTTACTGTAATTTTAC
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 3
-----------------------------gtaagtcattagaacttcatcctcttgtgtttga------ctccgatccatttaaaacatctctcgaataattcggtttcttgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC
| | || | || | |||| || | || ||||| | || | | | | | ||||||||||||||||||| |||||| || || |||||||| ||||| || || || || || || || ||||| || | |||||| ||||||| |||||| |||
gtaggttcctatgtgccattgtcgttcatatgatctccctgatttatatgccagtgtggttcatattatctttgatccctctagcttgttaataatgtttgtgtataatttgcagAAAAATCATATATTCACATCTGGGGCTTCTGGAACAAATGCAGCTGTTATTAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTAC
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------gtaagtcattagaacttcatcctcttgtgtttgact--ccgatccatttaaaacatctctcgaataatt---cggtttcttgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC
|| | | | | || | || ||| | | |||| | |||| | | | || | | ||| |||||||||||||||||||||| || |||||||| ||||||||||| || ||| ||||||| || || ||||||| ||| ||| ||||||| || || |||
gtaagtttctgttattttactctatagtatcatatgctttcttgtagtcttgtggaacacaatatatggtgaattggtgatgcagtatagttatgatttttgttaacaattccaatagctgtgtctcacaacttcttgtccatctgtttgtagAAAAATCATATATACACATCTGGAGCATCTGGGACTAATGCTGCTGTTATCCGAGGTGCTTTAAGGGCAGAGAAACCGGAGTTGCTTACTGTTATATTAC
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G00330.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------------------------gtaagtcattagaacttcatcctcttgtgtttgactccgatccatttaaaacatctctcgaataattcggtttcttgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC
|| | || || | || | |||| ||||| || | | || || | | | | ||| |||||||||||||||| ||||| || |||||||| ||||||||||| || || ||||||| || || ||||||| ||||||| |||||||||| || |||
gtaagttgttattttactcaagagtattatatgcttgcttgaagagtttcagtcttgtagaacacaatatatggtgaattggtgatgcagtactagttatgatttttgttaacaactccaatggctgtgtctcacaacttc--ttgtccatctgtttgtagAAAAATCATATATATACATCTGGAGCATCTGGGACTAATGCTGCTGTTATTCGAGGTGCTTTAAGGGCAGAGAAACCAGAGTTGCTTACAGTTATATTAC
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------gtaagtcatta--gaacttcatcctcttgtgtttgactccgatccatttaaaacatctctcgaataattcgg----tttcttgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC
|| || ||| || | | || || |||| | | | ||| ||| | | |||| | |||||||| || || | |||||||| |||||||| |||||||| || || ||||||||||| | |||||||||| ||||||||||||||| ||||| |||
gtatgatgctgtaacttctatcagtatattttatgtctaacattgtgggtgcttattgagcccaacatgctgctgggactctccattttcatattcatgcttctgaaattcctatgattatttcctacagAAAAACCACATTTTTACATCAGGAGCATCTGGCACTAATGCAGCTGTTATCAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTAC
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S134_28V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------gtaagtcattagaacttcatcctcttgtgtt---tgactccgatccatttaaaacatctctcgaataattcggtttcttgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC
| ||| | || | || || || | | | | | ||| || || ||| | ||| | ||| |||| ||||||||||| ||||| || ||| | ||||| ||||| || || || || || ||||||||||| || |||||||| || ||||| |||||||| |
tgctgtcagtgtaccttaatcagtactccaaaagtaattttccacaattccatcattgcagtgcatagaactcaactccttt-tcatttttctgtttgtagAATAATCATATATATACATCTGGAGCAGCGGGAACAAATGCGGCGGTTATAAGGGGAGCATTGAGAGCTGAAAGACCAGACCTTCTTACTGTAATTCTGC
upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S323_60V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------gtaa-gtcattagaacttcatcctcttgtgtttgactccgatccatttaaaacatctctcgaataattcggtttcttgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC
|| || || | | |||| ||| | | ||| | | | || | ||| | | || ||| || || |||||||||| || || |||||||| ||| | ||||| || || || || || || || ||||||||||| || |||||||| || ||||| ||||||||||
atacgaatcagagttctactgtcatgatatcgtaatcacagtttcacaaccttct--tcaacttcagtgc---tagaccatattt--aactcttctcttcgttttagAAAAATCACATTTATACATCAGGAGCAGCGGGAACAAACGCAGCTGTTATAAGGGGAGCATTGAGAGCTGAAAGACCAGACCTCCTTACTGTAATTCTACMapped 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|124812137|gb|EH897003.1|EH897003EST: TCATGCATCAAGAACTGATTGAGATACTTAGCTACGCCATGGTTATAACC AAAAATCATATATACA
genomic: TCATGCATCAAGAACTGATTGAGATACTTAGCTACGCCATGGTTATAACCgtaagtcatt ... tttcttgcagAAAAATCATATATACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtttgactccgatccatttaaaacatctctcgaataattcggtttcttgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC
gtttgac putative branch site (score: 4)
tttcttgc putative PPT
atttaaaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcattagaacttcatcctcttgtgtttgactccgatccatttaaaacatctctcgaataattcggtttcttgcagAAAAATCATATATACACATCAGGTGCATCTGGAACTAATGCTGCAGTCATCAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT