Sequence
atgc intronic sequence ATGC exonic sequence...acccttaaggttttaagatagtaaatgactctgaacgagtcggcgtagaaggatagtggcaggttttcatctgtctgttatggtacatgaatatgtgtagGCTCAGGTAGGAATGTTTTGTGGGCAAGAGATTGGAAATATATCAAGCTTTGCATCTTCCGGAGCTCCTTCAGACAATAGTAGCTCTCTTTGTGTTAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G24740.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 1
-acccttaaggttttaagatagtaaatgactctgaacgagtcggcgtagaaggatagtggcaggttttcatctgtctgt-tatg-gtacatgaatatgtgtagGCTCAGGTAGGAATGTTTTGTGGGCAAGAGATTGGAAATATATCAAGCTTTGCATCTTCCGGAGCTCCTTCAGACAATAGTAGCTCTCTTTGTGTTAAGG---------
||||| |||| | | | | | ||| | | | ||| || | | || | | || ||| | ||| | ||||||||||||||||||| |||||||||| |||||| ||| ||||| ||||||||||| |||| | | ||| | ||| ||||| | | |
agcccttgttatttttctgtgatgatt---tgtgattggggcaagtgcataggttattttccttttaactttaagtggtgcatgtatgggtgactgtgtgtagGCTCAGGTAGGATTGTTTTGTGGACAAGAGGTTGAGAATATTTCAAGCTTTGCTCCTTCAGAACATCCCCC---------TAGTTCTCTGTTTAAGGGAGTTGCTCGAA
upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 1
acccttaaggttttaagatagtaa--atgactctgaacgagtcggcg-tagaaggatagtggcaggttttcatctgtctgttat-----ggtacatgaatatgtgtagGCTCAGGTAGGAATGTTTTGTGGGCAAGAGATTGGAAATATATCAAGCTTTGCATCTTCCGGAGCTCCTTCAGACAAT---AGTAGCTCTCTTTGTGTTAAGG
|| | || | || | | | |||| | || |||| | ||||| | || | || | | ||| | ||||||||||||||||||| |||||||||| ||||| |||| | ||| ||||||||||| |||| | | ||| ||||| ||| | ||| ||||| | |||||
--------tattctgaggtggtggtgagagcataggttgagttaatgacagtgggatgacgttttgtttttaactatgagtggtacatgaatggatggctgtgtgtagGCTCAGGTAGGATTGTTTTGTGGACAAGATGTTGGGACTATTTCAAGCTTTGCTCCTTCAAGGGGTCCCTCAGAAAATACCACTAGTTCTCTATTTGTTA---
upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 1
acccttaaggttttaagatagta--aatgactctgaacgagtcggcg-tagaaggatagtggcaggttttc-atctgtctgttatg-gtacatgaata--tgtgtagGCTCAGGTAGGAATGTTTTGTGGGCAAGAGATTGGAAATATATCAAGCTTTGCATCTTCCGGAGCTCCTTCAGACAAT---AGTAGCTCTCTTTGTGTTAAGG
| || || | || | | | |||| | || |||| | |||| | || | || | | |||||| ||||||||||||||||||| |||||||||| ||||| |||| | ||| ||||||||||| |||| | | ||| ||||| || | ||| ||||| | |||||
-------atattccgaggtggtggtgagagcataggttgagttaatgacagtgggatgaagttttattttttaactatgagtggtacatgaatgaatggctgtgtagGCTCAGGTAGGATTGTTTTGTGGACAAGATGTTGGGACTATTTCAAGCTTTGCTCCTTCAAGGGGTCCCTCAGAACATACCACTAGTTCTCTATTTGTTA---
upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 1
-acccttaaggttttaagatagtaaatgactctgaacgagtcggcgtagaaggatagtggcaggttttcatctgtctgttatggtacatgaatatgtgtagGCTCAGGTAGGAATGTTTTGTGGGCAAGAGATTGGAAATATATCAAGCTTTGCATCTTCCGGAGCTCCTTCAGACAATAGTAGCTCTCTTTGTGTTAAGG---------
|||||| ||||| | | | | | | || ||| | | || | || | | | |||| | ||||||||||||||||||| |||||||||| |||||| ||| ||||| ||||||| ||| |||| | | ||| | ||| ||||| | | |
aacccttgttgtttttctgtgatgatttgtgattggggcaagtgcataggttatttttcttttaactttaagtggtgcatgta-tggatgactgtgtgtagGCTCAGGTAGGATTGTTTTGTGGACAAGAGGTTGAGAATATTTCAAGCTATGCTCCTTCAGAACATCCCCC---------TAGTTCTCTGTTTAAGGGAGTTGCCCGAA
upper sequence: AT4G24740.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 1
---acccttaaggttttaagatagtaaatgactctgaacgagtc-ggcgtagaaggatagtggcaggttttcatctgtctgttatggtacatgaatatgtgtagGCTCAGGTAGGAATGTTTTGTGGGCAAGAGATTGGAAATATATCAAGCTTTGCATCTTCCGGAGCTCCTTCAGACAA---TAGTAGCTCTCTTTGTGTTAAGG
| | | | ||| | ||| ||| | | || || | || || | | | || | | | | | ||| ||||||||||||||| |||| ||||||||||| |||||| |||| ||| | ||||||||||| |||| || | || ||| | || ||| ||| | | ||| |
aaaatcactgggagcttac--ttctaagggacaaggtatcagcgaggtacaaaattttaattttatatcttgagtggaacatga--atggatggctatgtgtagGCTCAGCTAGGGATGTTTTGTGGACAAGAGGTTGGGAATGTGGCAAGCTTTGCACCTTCAAAGGCACACTCCGACCAAACTACTAGTTCTATGTTTGTAA---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|124852047|gb|EH936484.1|EH936484EST: GCGTCTCGGTTGGGATGTGTTGCCTCAGGCAACCAAG GCTCAGGTAGGAATGTTTTGTGGGCAAGAGATTGGAAATATATCAAG
genomic: GCGTCTCGGTTGGGATGTGTTGCCTCAGGCAACCAAGgtataaattc ... atatgtgtagGCTCAGGTAGGAATGTTTTGTGGGCAAGAGATTGGAAATATATCAAG
EST:
gi|124874103|gb|EH955748.1|EH955748EST: CCAGAAAGAGAGCGCGTCTCGGTTGGGATGTGTTGCCTCAGGCAACCAAG GCTCAGGTAGGAATGTTTTGTGGGCAAGAGATTGGAAATATAT
genomic: CCAGAAAGAGAGCGCGTCTCGGTTGGGATGTGTTGCCTCAGGCAACCAAGgtataaattc ... atatgtgtagGCTCAGGTAGGAATGTTTTGTGGGCAAGAGATTGGAAATATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagaaggatagtggcaggttttcatctgtctgttatggtacatgaatatgtgtagGCTCAGGTAGGAATGTTTTGTGGGCAAGAGATTGGAAATATATCAAGCTTTGCATCTTCCGGAGCTCCTTCAGACAATAGTAGCTCTCTTTGTGTTAAGG
atgaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acccttaaggttttaagatagtaaatgactctgaacgagtcggcgtagaaggatagtggcaggttttcatctgtctgttatggtacatgaatatgtgtagGCTCAGGTAGGAATGTTTTGTGGGCAAGAGATTGGAAATATATCAAGCTTTGCATCTTCCGGAGCTCCTTCAGACAATAGTAGCTCTCTTTGTGTTAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
-cccttaa
- - - - ggtttta
- - - - - - - - - - - - - - - - - - - - - - - agaagga