Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtacacctcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatgggtttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G33210.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os03g04970.1 (Oryza sativa), 3'ss of exon 13
-gtaatgtacacctcttgtgaacatca--gactaataggctattaatgcattattagtt----tattactaatgtcgagattactcatatgggtt-tttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
|| | | || | | | | || | || | | | || || | || ||||| | | | | | | | || | |||||||||| ||||| ||||| | || ||| |||| ||||| |||||||| || ||||| |||||||| || ||||| || ||||||||||||||||| ||||
agtggcgga-acattctattactattactgattctagtgactgtcctgagttgtgagcatgggtattatttttttttaaaaaaattggatctttcctttagATTGGTGGAGCTAGTGAAGCGGAGGTTGGTGAGAAGAAGGATAGAGTGACTGATGCACTAAATGCTACCAAAGCTGCTGTAGAGGAGGGTATTGTACCAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 13
----gtaatgtacacctcttgtgaacatcagactaataggctattaatg-cattattagtttat-tactaatgtcgagattactcatatgggttttt--agATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
|||| | || | | | | |||| | || | | |||| | | | | | || |||| || | |||| |||||||| ||||| | |||||| |||| ||||| |||||||| || ||||| | |||||||||||||| || || || ||||||||||| ||||
acacacaatg-atgttgagaatggaagttgaattgcactgctaggagtggtgccctgaagttatattttgacctgtatatgcatcatgacctttcctacagATCGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCATTGAATGCCACTAAAGCTGCTGTGGAAGAGGGTATTGTACCAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G111477_T02 (Zea mays), 3'ss of exon 1
------------------------------gtaatgtacacc-tcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatggg------tttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
| | || | || ||||| | | || || || | || | | || | |||| || | || |||||||| ||||| || || |||||||| |||| ||||| |||||||| || ||||| || ||||| |||||||| || || || ||||||||||| ||||
gtgagattactgacctttgtatgtttactaatggcagattccatgtttcaaacattttttttctgttgtaatactgttacctgtgtctgtcctccatttgctgattttgtgcctgtgcctcctttcctagATTGGGGGAGCTAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGTATTGTACCAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 12
------------------------------------gtaatgtacac-ctcttgtga-acatcagactaatag--gctattaa-tgca-ttattagtttattactaatgtcgagattactcatatgggtttt--tagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
||| |||| |||||| | ||| | | || || ||| || | | | | || || || | | | || | ||| |||||||||||||| || || |||||||| |||| ||||| |||||||| || ||||| || ||||| |||||||| || || || ||||| ||||| ||||
gtgaggttattgacctactgtatgtatttacgaatggtagattacatgttcttgttttatatcgtaattgtaataactgttacctgtggctctctgatatttcctgattttgtgcctatgtgtgcatcctttcctagATTGGAGGAGCCAGCGAAGCAGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCACTGAATGCTACTAAAGCTGCTGTTGAAGAGGGCATTGTACCAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 13
---------gtaatgtacacctcttgtgaacatcagactaataggctattaatgcattattagtttattac--taatgtcgagattactcatatgggtttt-tagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
| || |||| || | || || || | | | ||| || ||| | | ||| | | || | | |||| ||||||||||||| |||||| | |||||| |||| ||||| |||||||| || ||||| ||||||| || || ||||| ||||||||||| || || ||||
gtttgtttatttgagtttaccttgcttgctgttaagtcttatctggtgcttcatcat-atggttttgtcatgataaaattaacatctgaaaccttacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 13
-----------gtaatgtacacctcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatgggtttt-tagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
| | ||| |||| | | | || ||| || || | | | | | | ||| | || | | |||| ||||||||||||| |||||| | |||||| |||| ||||| |||||||| || ||||| ||||||| || || ||||| ||||||||||| || || || |
gtttgtttatttgagtttaccttgcttgctattaggattttatctggcacttcatcctatggttttgtcatgataaaactaacatctgaaacctcacttttgcagATTGGAGGAGCCAGTGAGGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACCAAGGCAGCTGTAGAGGAGGGCATAGTACCTG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 13
gtaatgtacacct-cttgtgaacatcagactaataggctatt-------aatgcattattagtttattactaatgtcgagatt---actcata--tgggttttt--agATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
||| ||| |||||| | | |||| | ||| || | | | | | |||| | ||| | | | | || |||| ||||||||||||| ||||| | |||||| |||| ||||| |||||||| || ||||| ||||||| ||||| || || ||||||||||| || || || |
-----gtatgcctacttgtgtcattttggttaatggtttatccctggtgaacatcccactgaggttctgc-aatggaaaaattgacatttaaaactgcccttttgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACTGATGCATTAAATGCAACTAAGGCTGCTGTAGAGGAGGGCATAGTGCCTG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 13
-------gtaatgtacacctcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatgggtttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
| | | | | | | || | | | || || || || | || | || | | | ||||||||||||| ||||| | |||||| |||| ||||| |||||||| || ||||| ||||||| ||||| || || |||||||| || ||||| |||
gggggccgctacggccgctattgacaactatgatccctggtgaacatccctgtggggttctgcaatggcaaaattaacatttgaaactgcccttctgcagATTGGAGGAGCCAGTGAAGCTGAAGTTGGTGAGAAGAAGGATAGAGTGACAGATGCCTTAAATGCAACTAAGGCTGCTGTAGAGGAAGGCATTGTATCAG
upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 13
--------------------------------------------gtaatgtacacctcttgtgaac-atcagactaataggct-attaatg-----cattattagtttat-tactaatgtcgagattactcatatgggtttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
| | | | || || | | ||| || | ||| ||| |||| ||| || || | | | | | | ||| |||| |||||||| ||||| | ||||||||||| ||||||||||| || || |||||||||||||| ||||| ||||| ||||| || || ||||| ||||
gtctgtatcaatttacaaatccccaacattactgtctaggcttgttgaggctctaaactcaggagctactgtactggtactcagattcatggggaatgttatctagatatatataaaaatggtggaaaattgcttccctttgcagATAGGAGGAGCTAGTGAAGCTGAAGTTAGTGAGAAGAAAGATAGGGTTACAGATGCTCTAAATGCTACTAAGGCAGCTGTAGAAGAAGGAATTGTACCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaatgcattattagtttattactaatgtcgagattactcatatgggtttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
tactaat putative branch site (score: 1)
ttttt putative PPT
attattagtttattac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtacacctcttgtgaacatcagactaataggctattaatgcattattagtttattactaatgtcgagattactcatatgggtttttagATTGGAGGAGCAAGTGAGACAGAAGTTAGTGAAAAGAAAGATAGAGTAACGGATGCTCTAAATGCCACTAAAGCAGCCGTAGAGGAGGGTATTGTTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG