Sequence
atgc intronic sequence ATGC exonic sequencegtaagccgcatttcttctgatcctagttgctttcaggcacctgtgttgcttcacaagtcttatcaacaatgggcttttcggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G12980.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------------gtaagccgcatt-tcttctgatc--ctagttg-ctttcaggcacctgtgttg----cttcacaagtcttatcaacaatgggcttttcggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
|| | || | | || ||| | | | || | | || ||| ||| |||| || | ||||| | | ||||| ||||| ||||| |||| |||| | |||||||| | || || ||||||||||| ||||| ||| |||| ||||||||||| ||||| ||||||||||
gtaattcgctatgcctattgagttctcttcaatactttcttgtttagatttgtcaagaagaggggaatagtttcctaatcaatcactcgactaataatttctcgttttgataatttcttttgtctctaatactagttttttttctggatacagATAGGTTATCTTGAGTACTATAAGCAGCGTGGATTCACCAGTTGTTATATATGGGCTTGCCCTCCTGTTAAAGGTGAAGATTACATTTTGTATTGCCATC
upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 10
------------------------------------------------------------------------gtaagccgcatttcttct--gatcctagttgctttcaggcacctgtgttgcttcacaagtcttatcaacaatgggcttttcggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
||| || | || ||| || | | | | | | ||| | || || || | || | | | | ||||| || || ||||| || || ||| | |||||||| ||||||| || |||||||| ||||| ||| | || ||||||||||| ||||| || |||||||
gtaatgttctatgtttgctgagtttttctaaatttaaatgcgttgttttgccaggctggtcatactatttttgtatgcaactctttgggggggattctgccttcctccttaggctagcgtttttctgca---ctatctaatgctaggtctctatgtgttcagATAGGATATCTTGAATATTGCAAGCAGCGTGGATTCACAAGCTGTTACATATGGGCGTGCCCACCTTTAAAAGGTGAAGATTACATTTTGTACTGCCATC
upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 9
------------------------------------------------------------gtaagccgcatttcttctgatccta-----------gttgctttcaggcacctgtgttgctt-cacaagtcttatcaacaatgggctttt-cggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
| | | | | | || | | ||| | || | | ||| || || | ||| || | | | | ||||| || || ||||| ||||||||| || || || |||| || || |||||||| ||||| ||| | |||||||||||||| || |||||||||||||
gtaatttaccatccatgctgactttttgttgctagtacaaatttattgccttaccaggttttgatcaaaactgtctacgagaccatacaacaggaaaccttttttcttcttctttttagctagcatttgttctgggtctaatctgccctcaccgtgtacagATAGGATATCTTGAATACTGTAAGCTGCGGGGGTTCACAAGTTGTTACATATGGGCTTGCCCACCTTTGAAGGGTGAAGATTACATCTTATATTGCCATC
upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 10
----------------------------------------------------------------gtaagccgcatttcttctgatccta----gttgctttcaggcacctgtgttgcttcacaagtcttatcaacaatgggcttttcggattgc----agATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
| | | | | ||| | || ||| | ||| | | | | || || | || | | | | | | | || | || | ||||||| |||||||| || || ||||||||||| ||| |||||||||| ||||||||||| || || | |||||||||||||||||||||||||| ||||
gtaacctttagttctaattccttgtccttgtgttgggtggaatattatacagccttgtggaaccctttgttggagtcattcaagttctgatttgtttccttcctgtagttctatt-ctatataaatagt-tgagtagttttcgttatgattttcttttagATTGGATACCTTGAGTATTGCAAGAAACGTGGTTTTACAAGCTGCTACATATGGGCATGTCCTCCATTAAAGGGTGAAGATTATATTTTATATTGTCATC
upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 12
------------------------gtaagccgcatttcttctgatcctagttgctttcaggcacctgtgttgcttcacaagtcttatcaacaatgggcttttcggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
| | | | ||| | | | ||| || | | || || || | | | | | || || ||||||| |||||||| || || ||||||||||| ||| ||||||||||||| ||||| || || || | ||||| |||||||||||||||||||||||||
gtaaatttggacaccaagatgttgctttggcacccttccttagtgatattctagttttgggttattatcttcct--gtaaattatgtttgatacaaattatttctttt-tagATTGGATACCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCCTGTCCTCCATTAAAGGGAGAAGATTATATTTTATATTGCCATC
upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 10
------------------------gtaagccgcatttcttctgatcctagttgctttcaggcacctgtgttgcttcacaagtcttatcaacaatgggcttttcggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
| | || ||| | || | || || || | || || || | ||| ||| | || || ||||||| || ||||| || || ||||||||||| ||| ||||||||||||| ||||| || || || | ||||| |||||||||||||||||||||||||
gtaaatttggacactaagatcttgctttggagcccttccttagagatattctagttctgggttactatcttcct--gtaaattatatttgatatgaattatttctttt-tagATTGGATATCTTGAATATTGCAAGAAACGTGGTTTTACAAGCTGCTATATCTGGGCTTGTCCTCCATTAAAGGGGGAAGATTATATTTTATATTGCCATC
upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 9
-------------gtaagccgcatttcttctgatcctagttg-----ctttcaggcacctgtgttgcttcacaa-gtcttatcaaca---atgggcttttcggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
|| ||| || | | || || | || | | | | | | || | | | ||| | || | ||| || |||||||| || || || ||||||||||| || || || |||| |||||||||||||| || || ||| | ||||||||||| ||||| || ||||||||||
gtgagttttagtattacgccaatcttttatttattcttgatgagcaattcttatggtttggaatctttttatattgggctattggcttatatatccgattctctttccagATTGGATATCTCGAATACTGTAAGAAGCGGGGTTTCACAAGTTGCTATATATGGGCTTGTCCTCCTTTGAAGGGTGAAGACTATATATTGTATTGCCATC
upper sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S462_17V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------gtaagccgcatttcttctgatcctagttgctttcaggcacctgtgttgcttcacaagtcttatcaacaatgggcttttcggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
||| | | | || ||| | || |||| || | ||| || || ||| | | | || | |||||||| || || || || |||||| || | || ||| ||||| || || ||||| ||||| ||||| ||||| || ||||||||||||||||| ||||
aattttttttctttacttaaaatgtagtgctgctgtttct-gttg--ttacgttgtttgtactggcagaccagttgaacttgttggcgtatgatctg-ttgcagATCGGCTATCTAGATTACTGTCGGAGGAGAGGTTTTAGTAGCTGTTACATTTGGGCTTGCCCACCTCTAAAGGGAGAGGATTATATTTTATATTGTCATCMapped 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|125185570|gb|EL200524.1|EL200524EST: TATCTGGAGAGGCCCTCCGTACGTTCGTATACCATGAAATTCTG ATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAAGCTGCTATAT
genomic: TATCTGGAGAGGCCCTCCGTACGTTCGTATACCATGAAATTCTGgtaagccgca ... cggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAA-GCTGCTATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caggcacctgtgttgcttcacaagtcttatcaacaatgggcttttcggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
cttttc CT-rich tract
ttatcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagccgcatttcttctgatcctagttgctttcaggcacctgtgttgcttcacaagtcttatcaacaatgggcttttcggattgcagATTGGTTACCTTGACTACTGTAAGAAACGTGGATTTTCAAGCTGCTATATATGGGCATGCCCCCCTCTTAAGGGTGAAGATTATATTTTATATTGCCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA