Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttctttgattcttacatgtttcgtttaagacttttcttacctgaggtttagctgtgcaatgtggtgttggcattattgtttcttggaagattgtggtggcatttatggtagacacaatgtttgtcttttgttttgtagTGATTGTGGGGGAAATTGCAAACTTTGCTGCGTATGCGTTTGCACCTGCCATTCTAGTTACTCCTCTTGGTGCGCTTAGCATTATTATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G09640.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G09640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 2
gtgagtttctttgattcttacatgtttcgtttaagacttttcttacctgaggtttagctgtgcaatgtggtgttggcattattgtttcttggaagattgtggtggcatttatggtagacacaatgtttgtcttttgttttgtagTGATTGTGGGGGAAATTGCAAACTTTGCTGCGTATGCGTTTGCACCTGCCATTCTAGTTACTCCTCTTGGTGCGCTTAGCATTATTATCAG
| | | |||| ||| |||| || || | || | | | || | || | | | |||| || | || | ||||| |||||||||||| ||||||||||| |||||||| ||||| ||||| ||||| ||||| |||||||||||||| || || || || || |||||
-------------------------------------tctaatatactgaagtt--actgtttcatttgtttttagacaaaaaatgtcactaaggaaagaaacttgactaatgg----catcttacatgacctttgtga-acagTGATTGTGGGAGAAATTGCAAATTTTGCTGCTTATGCATTTGCTCCTGCTATTCTTGTTACTCCTCTTGGGGCACTCAGTATAATCATCAG
upper sequence: AT4G09640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G129268_T01 (Zea mays), 3'ss of exon 2
gtgagtttctttgattcttacatgtttcgtttaagacttttcttacctgaggtttagctgtgcaatgtggtgttggcattattgtttcttggaagattgtggtggcatttatggtagacacaatgtttgtcttttgttttgtagTGATTGTGGGGGAAATTGCAAACTTTGCTGCGTATGCGTTTGCACCTGCCATTCTAGTTACTCCTCTTGGTGCGCTTAGCATTATTATCAG
| | ||| | ||| | ||| | || || | || | || || | || | | || || || | ||| |||||| ||||||||| || |||||||| || |||||||| ||||| || || ||||| ||||| || |||||||||||||| || || || || |||||
---------------------------tgcacagaactgctgctac--aaccttttttaggagaacatgttactgaa------gctttctgaatga-----aagaaacttgaaatatgtacg-tacatgtgttttgt---acagTGATTGTAGGTGAAATTGCTAATTTTGCTGCTTATGCATTCGCTCCTGCTATTCTTGTCACTCCTCTTGGTGCACTCAGTATAATCATCAG
upper sequence: AT4G09640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G104147_T02 (Zea mays), 3'ss of exon 2
gtgagtttctttgattcttacatgtttcgtttaagacttttcttacctgaggtttagctgtgcaatgtggtgttggcattattgtttcttggaagattgtggtggcatttatggtagacacaat-gtttgtcttttgttttgtagTGATTGTGGGGGAAATTGCAAACTTTGCTGCGTATGCGTTTGCACCTGCCATTCTAGTTACTCCTCTTGGTGCGCTTAGCATTATTATCAG
|| | | || | | | | | || | | | || || | || | | | || | || | |||||||||| ||||||||| || |||||||| || |||||||| ||||| || || || || ||||| || |||||||||||||| || || || || || ||
-----------------------------------------------tgctact-atcttttctaggagtacctgttactcaagctttctgaatga-----gagaaacttgaaatgtgttcacttacatgtcttttgtgc-acagtgattgtagGTGAAATTGCTAATTTTGCTGCTTATGCATTCGCTCCAGCTATTCTTGTCACTCCTCTTGGTGCACTAAGTATAATCATAAG
upper sequence: AT4G09640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G104147_T03 (Zea mays), 3'ss of exon 2
gtgagtttctttgattcttacatgtttcgtttaagacttttcttacctgaggtttagctgtgcaatgtggtgttggcattattgtttcttggaagattgtggtggcatttatggtagacacaat-gtttgtcttttgttttgtagTGATTGTGGGGGAAATTGCAAACTTTGCTGCGTATGCGTTTGCACCTGCCATTCTAGTTACTCCTCTTGGTGCGCTTAGCATTATTATCAG
|| ||| | ||| || || | | | | | || | | | || || | || | | | || | || | |||||||||| ||||||||| || |||||||| || |||||||| ||||| || || || || ||||| || |||||||||||||| || || || || || ||
-------------------------------caaaactgctgctac--------tatcttttctaggagtacctgttactcaagctttctgaatga-----gagaaacttgaaatgtgttcacttacatgtcttttgtgc-acagTGATTGTAGGTGAAATTGCTAATTTTGCTGCTTATGCATTCGCTCCAGCTATTCTTGTCACTCCTCTTGGTGCACTAAGTATAATCATAAG
upper sequence: AT4G09640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ16080 (Selaginella moellendorffii), 3'ss of exon 2
gtgagtttctttgattcttacatgtttcgtttaagacttttcttacctgaggtttagctgtgcaatgtggtgttggcattattgtttcttggaagattgtggtggcatttatggtagacacaatgtttgtcttttgttttg--tagTGATTGTGGGGGAAATTGCAAACTTTGCTGCGTATGCGTTTGCACCTGCCATTCTAGTTACTCCTCTTGGTGCGCTTAGCATTATTATCAG
|| | | | || | | | | | | |||| ||||| | |||| |||||| | || || ||||||||||||| |||||||||||||| ||||| || || || || ||| | || || | || ||||| | ||
-----------------------------------------------------------------------------------gtaagctagtttgtccaggatgaaaatgcgaaata-acaaagtttgctcacttctttgagcagTGATATTTGGCGAGGTTGCAAACTTTGCAGCGTATGCGTTTGCTCCTGCGATACTTGTCACGCCTTTAGGAGCTTTGAGTATTATAGTAAG
upper sequence: AT4G09640.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ15113 (Selaginella moellendorffii), 3'ss of exon 2
gtgagtttctttgattcttacatgtttcgtttaagacttttcttacctgaggtttagctgtgcaatgtggtgttggcattattgtttcttggaagattgtggtggcatttatggtagacacaatgtttgtcttttgttttgtagTGATTGTGGGGGAAATTGCAAACTTTGCTGCGTATGCGTTTGCACCTGCCATTCTAGTTACTCCTCTTGGTGCGCTTAGCATTATTATCAG
|| || || | |||| ||| || || | || ||| | | | || || | |||||| | || || ||||||||||||| |||||||||||||| ||||| || || || || ||| | || || | || ||||| | ||
-----------------------------------------------------------------------gtaagc--tagtttttccaggatgaaaatg-cgaaat--------aacaaagtttgctcacttctttgagcagTGATATTTGGCGAGGTTGCAAACTTTGCAGCGTATGCGTTTGCTCCTGCGATACTTGTCACGCCTTTAGGAGCTTTGAGTATTATAGTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaagattgtggtggcatttatggtagacacaatgtttgtcttttgttttgtagTGATTGTGGGGGAAATTGCAAACTTTGCTGCGTATGCGTTTGCACCTGCCATTCTAGTTACTCCTCTTGGTGCGCTTAGCATTATTATCAG
tttgtcttttgtttt CT-rich tract
ttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttctttgattcttacatgtttcgtttaagacttttcttacctgaggtttagctgtgcaatgtggtgttggcattattgtttcttggaagattgtggtggcatttatggtagacacaatgtttgtcttttgttttgtagTGATTGTGGGGGAAATTGCAAACTTTGCTGCGTATGCGTTTGCACCTGCCATTCTAGTTACTCCTCTTGGTGCGCTTAGCATTATTATCAG
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