Sequence
atgc intronic sequence ATGC exonic sequencegtgagtaagattgtctatcttgttgttttaccattggttaagattcccaaacattttatgtctccttgtggtagGCTAAATGCAGAGAAACTGGGGAGGTTGTTGCCATCAAAAAAGTTCTACAAGACAAGCGTTACAAGAACAGAGAATTACAAATTATGCAGATGCTAGACC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G57870.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 4
----gtgagtaagattgtctatcttgttgttttaccat-tggttaagattcccaaacattttatgtct-ccttgtggtagGCTAAATGCAGAGAAACTGGGGAGGTTGTTGCCATCAAAAAAGTTCTACAAGACAAGCGTTACAAGAACAGAGAATTACAAATTATGCAGATGCTAGACC
| || || || | | ||| | || || | || |||| | | | | | | ||||| ||||| ||||||| || || |||||||||| ||||| ||||| ||||| || |||||||||||||| ||||| ||||||||||| ||||| || |
gtaagcctgtggctttttcattgtaaaaatttctctatgtgactgtgaaaggcaaataacctgttcgtgtcaactcttagGCCAAATGTCGAGAAACAGGAGAAATTGTTGCCATTAAAAAGGTTCTTCAAGATAAACGTTACAAGAACAGGGAATTGCAAATTATGCATATGCTGGATC
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G138676_T03 (Zea mays), 3'ss of exon 4
gtgagtaa---gattgtctatctt----gttgttttaccattggttaagattcccaaacattttat-gtctccttgtgg------tagGCTAAATGCAGAGAAACTGGGGAGGTTGTTGCCATCAAAAAAGTTCTACAAGACAAGCGTTACAAGAACAGAGAATTACAAATTATGCAGATGCTAGACC
|| | || | ||| | || |||| || | || | | | || || | | | || | | ||||| |||||| ||||||| ||||| |||||||||| ||||| || || ||||| |||||||| ||||||||||| | ||||| ||||| ||||| ||||
gtaaacaacccacctttctgttttctgtactgttctatgcctaattgatagtgaaaagcacataaccatttcatcattaactctttagGCAAAATGCCGAGAAACAGGGGAAATTGTTGCCATAAAAAAGGTCCTTCAAGATAAGCGTTATAAGAACAGAGAGCTGCAAATCATGCATATGCTTGACC
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G00400.2 (Glycine max), 3'ss of exon 3
--------------gtgagtaagattgtctatcttgttgttttaccattggttaagat-tcccaaacattttatgtctccttgtggtagGCTAAATGCAGAGAAACTGGGGAGGTTGTTGCCATCAAAAAAGTTCTACAAGACAAGCGTTACAAGAACAGAGAATTACAAATTATGCAGATGCTAGACC
|| | || | | | | || || ||| | | | ||| | |||||||| | ||| | |||| ||||| |||||||| || || |||| |||||||| |||||||| || |||||||| |||||||| ||||| |||||||||||||| ||||| || |
gtgagttttcttttgtaaaccccatcttgtttatcgtatttcagacat-gctgatgataccttcttcattttattaatgcttttatcagGCCAAATGTAGAGAAACGGGAGAAATTGTGGCCATCAAGAAAGTTCTCCAGGACAAGCGCTACAAGAATAGAGAGTTACAAATTATGCAAATGCTGGATC
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 4
-----------------gtgagtaagattgtctatcttgttgttttaccat-tggttaagattcccaaa-cattttatgtctccttgtggtagGCTAAATGCAGAGAAACTGGGGAGGTTGTTGCCATCAAAAAAGTTCTACAAGACAAGCGTTACAAGAACAGAGAATTACAAATTATGCAGATGCTAGACC
| | | | || ||||| | || | | | | ||| || | |||||| | ||| | ||||| ||||| |||||||| || || |||| |||||||| |||||||| || ||||| || |||||||| ||||| |||||||||||||| ||||| || |
gtgagtttgcttttcatatctcttctaaacaccatgctgttgatgtatgacatactgatgataccttcttcgttttatcaatgcttttattagGCAAAATGTAGAGAAACAGGAGAAATTGTGGCCATCAAGAAAGTTCTCCAGGACAAACGATACAAGAATAGAGAGTTACAAATTATGCAAATGCTGGATC
upper sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 3
----------------------gtgagtaagattgtctatcttgttgttttaccattggttaagattcccaaacattttatgtctccttgtggtagGCTAAATGCAGAGAAACTGGGGAGGTTGTTGCCATCAAAAAAGTTCTACAAGACAAGCGTTACAAGAACAGAGAATTACAAATTATGCAGATGCTAGACC
| | ||| || ||| |||| | || || | | | | | | ||| | || ||| |||| ||||| ||||| ||||| ||| |||| |||||||| || ||||| ||||||||||| |||||||| || || ||||| |||||||| ||| | ||||
gtaagcagaacttctttggtttttcttttgaatttactttctaaaccttttgcagttattttacagtg--agatagtttttaactgctttgttcagGCAAAATGTAGAGAGACTGGAGAGATTGTCGCCATCAAGAAGGTTCTCCAAGACAAGCGCTACAAGAATAGGGAGTTACAGATTATGCAAATGTTGGACCMapped 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|116396564|gb|EG439156.1|EG439156EST: ACATAGCAGAACACGTAGTCGGGACTGGTTCATTCGGAATGGTTTTCCAA GCTAAATGCAGAGAAACTGGGGAGGTTGTTGCCATCNNNNNNNGTTCTACA
genomic: ACATAGCAGAACACGTAGTCGGGACTGGTTCATTCGGAATGGTTTTCCAAgtgagtaaga ... cttgtggtagGCTAAATGCAGAGAAACTGGGGAGGTTGTTGCCATCAAAAAA-GTTCTACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttgttttaccattggttaagattcccaaacattttatgtctccttgtggtagGCTAAATGCAGAGAAACTGGGGAGGTTGTTGCCATCAAAAAAGTTCTACAAGACAAGCGTTACAAGAACAGAGAATTACAAATTATGCAGATGCTAGACC
ttttatgtctcctt CT-rich tract
aaacattttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtaagattgtctatcttgttgttttaccattggttaagattcccaaacattttatgtctccttgtggtagGCTAAATGCAGAGAAACTGGGGAGGTTGTTGCCATCAAAAAAGTTCTACAAGACAAGCGTTACAAGAACAGAGAATTACAAATTATGCAGATGCTAGACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG