Sequence
atgc intronic sequence ATGC exonic sequence...gcattatgcatagctctttcatggtaatagcttgcttgattcttaaattgcattaatgttgattcttcttcttgatatgtgtattgatatgtgtatacagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGATTTCTATTACGCATGTGGTATGCTCGGAGATGCTTTCAAGAACTATATCC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61140.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g02540.1 (Oryza sativa), 3'ss of exon 1
gcattatgcatagctctttcatg-gtaatagcttgcttgattcttaaattgcattaatgttgattctt-cttcttgatatgtgtattgatatgtgtat-acagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGATTTCTATTACGCATGTGGTATGCTCGGAGATGCTTTCAAGAACTATATCC
| | | || | | || ||| | | || | | | | ||| || || || ||| | || | | ||| | || ||||| || | ||||| || |||||||||||||||||||||||| |||| ||||||| || || ||| || |||||| ||||| | ||| ||||
--ttgctttgtggccttgttgtgcgtacttctattctaaggtgatggcatac-ttattgaagaaactaacttttctggatttattttgtttctcaaattgcagACCAACCTTATCAAAGAGAGCATCAGAATGGGTTACAATGACATTGGTGATTTCTTCTATGCTCATGGCCACCTTTCAGATGCCTTCAAAAGCTACATCC
upper sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G153152_T01 (Zea mays), 3'ss of exon 1
gcattatgcatagctctttcatggtaatagcttgcttgattcttaaattgcattaatgttgattcttctt--cttgatatgtgtattgatatgtgta-tacagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGATTTCTATTACGCATGTGGTATGCTCGGAGATGCTT--TCAAGAACTATATCC
||| | | | | ||| || | | | || | | || || || | ||| || | |||||| || | ||||| || || ||||| || |||||||||||||| ||||||||| |||| ||||||| || || ||| || | | ||| ||| ||
--attgtcctcgtgcgcagaacgtcaatc-ctcagaaaaatgtccttgtgtgatgacgtcaatcctctataactttcaatctacattgattctcttactgcagACTAACTTAATCAAAGAGAGCATCAGAATGGGCTACAATGACATTGGCGATTTCTTCTATGCCCATGGCCAACTTTCAAAAGCTACATCAGGACTCGGGA--
upper sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G062210_T02 (Zea mays), 3'ss of exon 1
gcattatgcatagctctttcatggtaatagcttgct--tgattcttaaattgcat-taatgttgattct-tcttcttgatatgtgtattgatatgtgta-tacagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGATTTCTATTACGCATGTGGTATGCTCGGAGATGCTTTCAAGAACTATATCC
|| ||| | || |||| ||| | ||| | ||| || || ||| || | || | |||||| || | ||||| || || ||||| || |||||||||||||| ||||||||| |||| ||||||| || || ||| || |||||||||||| | ||| |||
-----atttcccattctaaagcgacaagtgcttatcaatgaaaatgccattctgcatgttgtcaatcctctctaattcaaatctacattgattctcttactgcagACTAACTTAATCAAAGAGAGCATCAGAATGGGCTACAATGACATTGGTGATTTCTTCTATGCCCATGGCCAACTTTCAGATGCTTTCAAAAGCTACATCA
upper sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G01880.1 (Glycine max), 3'ss of exon 1
---gcattatgcatagctctttcatggtaatagcttgcttgattcttaaattgcattaatgttgattcttcttcttgatatgtgtat-tgatatgtgtat---acagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGATTTCTATTACGCATGTGGTATGCTCGGAGATGCTTTCAAGAACTATATCC
| | | | ||| ||| ||| || ||||| ||| ||||| || | || | | || | | || ||| || | || | | | |||||||| || || ||||||||||| |||||||| |||||||| |||||||| || || || || |||| | || || ||||| || | ||| |||
ataggactgtaggtagtattttgatga----ggcctgcttt-ttcgtaaat--caccattgattccttatcctgtcaatttgttcatcttgcatttattttttgcagACAAACTTAATTAAGGAAAGCATTAGAATGGGATACAATGATTTTGGAGAGTTTTACTATGCTCATGGTCAATTGGGGGACGCTTTTAAAAGTTATGTCC
upper sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G08370.1 (Glycine max), 3'ss of exon 1
-----gcattatgcatagctctttcatggtaatagcttgcttgattcttaaattgcattaatgttgattcttcttcttgatatgtgtattg-atatgtgtat-acagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGATTTCTATTACGCATGTGGTATGCTCGGAGATGCTTTCAAGAACTATATCC
| | ||| || ||| ||||| | || || ||| |||||| || | || | | || | | || ||| || | || | | | | |||||||| ||||| ||||||||||| || ||||| | |||||| |||||||| || || || || |||| | || || ||||| || | ||| |||
aataaggacaatgaggagtatttt---ggtaagacctgtttt--ttcgtaaatt--atcattgattccttatcctgtcaatttgttcatcgcatttattttttgcagACAAACTTGATTAAGGAAAGCATTAGGATGGGATTCAATGATTTTGGAGACTTTTACTATGCTCATGGTCAATTGGGGGACGCTTTTAAAAGTTATGTCC
upper sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0048g01980.t01 (Vitis vinifera), 3'ss of exon 1
gcattatgcatagctctttcatggtaatagcttgcttgattcttaaattgcattaatgttgattctt--cttcttgatatgtgtattgata-tgtg------tatacagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGATTTCTATTACGCATGTGGTATGCTCGGAGATGCTTTCAAGAACTATATCC
| | | | || | || | | | | | ||| || | | ||||| ||| | || || | | || |||| | | ||||||||||| ||||| |||||||| |||||||| ||||||||||| |||||||| || || || ||| | || | |||||||| ||||| ||| | |
--------ttttggtaggttataggggtaacgtacctt-tgtgcgaatggctgaagtacccattctgaatttcataatttgcctccttatggtgtgatcctttctgcagACAAATTTAATCAAAGAAAGCATAAGAATGGGATACAATGACTTCGGAGATTTTTACTATGCCCACGGTTTACTTGCGGATGCTTTTAAGAATTATGTTCMapped 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|125042821|gb|EL115090.1|EL115090EST: CTGGAGAATGAGCTCAGTTCTTATCGG ACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGAT
genomic: CTGGAGAATGAGCTCAGTTCTTATCGGgtaattacat ... gtgtatacagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGAT
EST:
gi|124858076|gb|EH942513.1|EH942513EST: TGCTGAACAGAAGAAAGTAAAGCTGGAGAATTGAGCTCAGTTCTTATCGG ACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAA
genomic: TGCTGAACAGAAGAAAGTAAAGCTGGAGAA-TGAGCTCAGTTCTTATCGGgtaattacat ... gtgtatacagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAA
EST:
gi|19877543|gb|AU238374.1|AU238374EST: GTGCTGAACAGAAGAAAGTAAAGCTGGAGAATGAGCTCAGTTCTTATCGG ACAAATTTTATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGAT
genomic: GTGCTGAACAGAAGAAAGTAAAGCTGGAGAATGAGCTCAGTTCTTATCGGgtaattacat ... gtgtatacagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgcattaatgttgattcttcttcttgatatgtgtattgatatgtgtatacagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGATTTCTATTACGCATGTGGTATGCTCGGAGATGCTTTCAAGAACTATATCC
tattgat putative branch site (score: 3)
attaatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcattatgcatagctctttcatggtaatagcttgcttgattcttaaattgcattaatgttgattcttcttcttgatatgtgtattgatatgtgtatacagACAAATTTGATCAAGGAAAGCATCAGAATGGGTTACAATGACTTTGGAGATTTCTATTACGCATGTGGTATGCTCGGAGATGCTTTCAAGAACTATATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC