Sequence
atgc intronic sequence ATGC exonic sequence...cacggttcttgaaatgagttgaaaataaatgcaaatcttgattttgccatgtgatagatttatggttatactaatcgtttatattaatgttgtgttgtagGATTTCATCAATGTAGATGGGGATACCATAATCTATCAGTTGTTGAAGATGTGGTGGATAATTACAAAAAGGCTAAGATCCCACTTGATGTGATTTGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G68560.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G68560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G31890.1 (Glycine max), 3'ss of exon 2
cacggttcttgaaatgagttgaaaataaatgcaaatcttgattttgccatgtgatagatttatggttatactaatcgtttat--attaatgttgtgttgtagGATTTCATCAATGTAGATGGGGATACCATAATCTATCAGTTGTTGAAGATGTGGTGGATAATTACAAAAAGGCTAAGATCCCACTTGATGTGATTTGGAA
| |||| || || | | || | | | | | || | | | | || | | | | ||| | |||| | || || ||||||| || ||||||||||||||||| || |||||||| || ||||||||||| ||||| |||||||| |||||| | |||||||||||||||||||||||
-ttagcatttgatttgtatt-attccagatctagttgatagtggtacctaaagtttttctaaaagtagtttaactgatatatccactaatttggtattatagGATTCCACCAATGTAGATGGGGATATCACAATCTATCTGTGGTTGAAGATGTTGTGGAGAATTACAAGAAGGCTCAAATCCCACTTGATGTGATTTGGAA
upper sequence: AT1G68560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G20460.1 (Glycine max), 3'ss of exon 2
cacggttcttgaaatgagttgaaaataaatgcaaatcttgattttgccatgtgatagatttatggttatactaatcgtttat--attaatgttgtgttgtagGATTTCATCAATGTAGATGGGGATACCATAATCTATCAGTTGTTGAAGATGTGGTGGATAATTACAAAAAGGCTAAGATCCCACTTGATGTGATTTGGAA
|| ||| | | | | ||| || | || | | || | | | | | || | | | | ||| | | || | || || ||||||| || || || ||||||||||| || ||||||||||| || |||||||| ||||| |||||||| |||||| | ||||||||||||||||| |||||
-actgttatatcattcacatgaggctactt-catttgtcagttaaatgaaaggtttttctaaaagtagtttaactgatatattcacttatttggtattatagGATTCCACCAGTGCAGATGGGGATATCACAATCTATCAGTGGTAGAAGATGTTGTGGAGAATTACAAGAAGGCTCAAATCCCACTTGATGTGATCTGGAA
upper sequence: AT1G68560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G42140.1 (Glycine max), 3'ss of exon 2
--cacggttcttgaaatgagttgaaaataaatgcaaatcttgattttgccatgtgatagatttatggttatactaatcgtttatattaatgttgtgttgtagGATTTCATCAATGTAGATGGGGATACCATAATCTATCAGTTGTTGAAGATGTGGTGGATAATTACAAAAAGGCTAAGATCCCACTTGATGTGATTTGGAA
| | | || | | || | | |||| || | | || | | | ||| || | | | || | | | || ||||||| || ||||| |||||||| || || |||||||| ||||| |||||||| || || |||||||| ||||| || ||||||||||||||||| |||||
tgcttgtctgccagaacta-tcatttgtatgaagagaacttgtttgtaaaaggtacttggcaaacatgctcacttattttattt-ttggtataatattatagGATTCCACCAATGCAGATGGGGCTATCACAATCTATCCGTTGTAGAAGATGTTGTCGAGAATTACAAGAAGGCAAAAATCCCACTTGATGTGATCTGGAA
upper sequence: AT1G68560.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0011g03450.t01 (Vitis vinifera), 3'ss of exon 2
---cacggttcttgaaatgagttgaaaataaatgcaaatcttgattttgccatgtgatagatttatggttatactaat-cgtttatattaatgttgtgttgtagGATTTCATCAATGTAGATGGGGATACCATAATCTATCAGTTGTTGAAGATGTGGTGGATAATTACAAAAAGGCTAAGATCCCACTTGATGTGATTTGGAA
|| |||||| || | | | || || | | | | | || || || | || || ||| | || ||| ||||| ||||||| || |||||||||||||| |||||||||||||| || |||||||||||||| || || |||||||||||| | ||||| ||||||||||| |||||
aggcatggttctaaaagacatcttg---tggttgaaattggtcgtctagaaatcct-tattttgagaaaatcaccaacatttttttttttttgtggtgttatagGATTCCACCAATGTAGATGGGGTTACCATAATCTATCTGTAGTTGAAGATGTGGTTGAGAACTACAAAAAGGCTCAAATCCCGCTTGATGTGATATGGAAMapped 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|164179935|gb|ES052441.1|ES052441EST: ACTCAGTTAATCGGAAGACCTGCTCCTATGCCGTACTGGTCTTTAG GATTTCATCAATGTAGATGGGGATACCATAATCTATCAGTTGTTGAAGATG
genomic: ACTCAGTTAATCGGAAGACCTGCTCCTATGCCGTACTGGTCTTTAGgtatgttcat ... tgtgttgtagGATTTCATCAATGTAGATGGGGATACCATAATCTATCAGTTGTTGAAGATG
EST:
gi|124773307|gb|EH863436.1|EH863436EST: TCGGAAGACCTGCTCCTATGCCGTACTGGTCTTTAG GATTTCATCAATGTAGATGGGGATACCATAATCTATCAGTTGTTGAAGATG
genomic: TCGGAAGACCTGCTCCTATGCCGTACTGGTCTTTAGgtatgttcat ... tgtgttgtagGATTTCATCAATGTAGATGGGGATACCATAATCTATCAGTTGTTGAAGATG
EST:
gi|164050717|gb|ES205542.1|ES205542EST: GTATACTCAGTTAATCGGAAGACCTGCTCCTATGCCGTACTGGTCTTTAG GATTTCATCAA
genomic: GTATACTCAGTTAATCGGAAGACCTGCTCCTATGCCGTACTGGTCTTTAGgtatgttcat ... tgtgttgtagGATTTCATCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccatgtgatagatttatggttatactaatcgtttatattaatgttgtgttgtagGATTTCATCAATGTAGATGGGGATACCATAATCTATCAGTTGTTGAAGATGTGGTGGATAATTACAAAAAGGCTAAGATCCCACTTGATGTGATTTGGAA
ttatactaatcgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cacggttcttgaaatgagttgaaaataaatgcaaatcttgattttgccatgtgatagatttatggttatactaatcgtttatattaatgttgtgttgtagGATTTCATCAATGTAGATGGGGATACCATAATCTATCAGTTGTTGAAGATGTGGTGGATAATTACAAAAAGGCTAAGATCCCACTTGATGTGATTTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - -caaatct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actaatc