Sequence
atgc intronic sequence ATGC exonic sequencegtaaaggcttttagagaattcctctgtaatctctgtatttctaaggatgaatagccaatcattgagtgttacggttaccagATTGCAGATGTATGGTCATGTGGTGTGACCTTATACGTCATGTTGGTTGGAGCGTATCCGTTCGAAGATCCAGAAGAGCCAAGAGACTATCGGAAAACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G66880.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 6
---------------------gtaaaggcttttagagaattcctctgtaatctctgtatttctaaggatgaatagccaatcattgagtgttacggttaccagATTGCAGATGTATGGTCATGTGGTGTGACCTTATACGTCATGTTGGTTGGAGCGTATCCGTTCGAAGATCCAGAAGAGCCAAGAGACTATCGGAAAACAA
| | | ||| | | | | | |||| | | ||| | |||| | | | | |||| ||| ||||||||||| ||||||||||| |||| || ||| | ||||| || ||||| ||||| |||||||||||||| | ||| || |||||||
tgtcccttctttttctttaaaacagaagtatttccattactgataaccgcttagtgtaggaatcctggctcatactgatacattatttatactga--aacagACTGCTGATGTATGGTCCTGTGGTGTGACTCTATATGTTATGGTAGTTGGTGCATATCCTTTCGAGGATCCAGAAGAGCCTAAGAACTTCCGTAAAACAA
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 3'ss of exon 6
-----------gtaaaggctt--ttagagaattcctctgtaatctctgtatttctaaggatgaat-agc-caatcattgag----tgttacggttaccagATTGCAGATGTATGGTCATGTGGTGTGACCTTATACGTCATGTTGGTTGGAGCGTATCCGTTCGAAGATCCAGAAGAGCCAAGAGACTATCGGAAAACAA
|| ||| | ||| | || ||| | | ||| | | || | | ||| ||||| | | ||| | ||||||| ||||| |||||||| |||||||| | ||||| ||||||||||| || || || ||||| ||||| ||||| || | ||| | || ||||
tgatccatgtttcaatggcatgggtagtgtatggtcttgtgaagtaacccttttaatgcattagttagctcaatccctaataatttgtctttggatggagATTGCCGATGTTTGGTCATGCGGTGTGACGCTCTACGTGATGTTGGTTGGCGCATACCCTTTCGAGGATCCTGAAGATCCCAAGAACTTCAGAAAGACAA
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 7
------------gtaaaggcttttagagaattc-ctctgtaatctctgtatttctaaggatgaatagccaatcattgagtgttacggttac-------cagATTGCAGATGTATGGTCATGTGGTGTGACCTTATACGTCATGTTGGTTGGAGCGTATCCGTTCGAAGATCCAGAAGAGCCAAGAGACTATCGGAAAACAA
| | || || || ||| || | | | | | | | |||| | | ||| || | | | |||| |||||||| || || |||||||||||||| ||| | || || ||| | ||||| || ||||| || ||||||||||||||||| | ||| || || ||||
aaacttccacttatgatttctcttttagtgttcactgtctggttacctcctatatgagga-aagcttctcctcaccgatggatttgtttacgacaaaacagATTGCTGACGTTTGGTCATGTGGTGTAACCCTCTATGTAATGGTTGTTGGCGCATATCCTTTTGAAGATCCAGAAGAGCCTAAGAACTTCCGCAAGACAA
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S218_59V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------------------------gtaaaggcttttaga---gaattcctctgtaatctctgtatttctaaggatgaatagc-------caatcattgag-------tgttacggttaccagATTGCAGATGTATGGTCATGTGGTGTGACCTTATACGTCATGTTGGTTGGAGCGTATCCGTTCGAAGATCCAGAAGAGCCAAGAGACTATCGGAAAACAA
|| | | || ||| | | | | || || || || | || || | ||| || | | |||||||||||||| ||||| || ||||| ||||| ||||| |||||||||||||| ||||| ||||| ||||| ||||| ||||| | | ||||||| |
gtaagtttttcggaagcgtgttggttttagtggaataaattggttcttggacaatgctattatcatgcggaactgaagctatttttggtgtcggtgaggttacaagtgcacggctctttgtcagctaaagaggctgatttgccgtgatatacagATTGCAGATGTGTGGTCTTGCGGTGTTACCTTGTACGTGATGTTGGTTGGAGCATATCCTTTCGAGGATCCTGAAGACCCAAGGAATTTCAGGAAAACCA
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S113_72V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------gtaaaggcttttagagaattcctctgtaatctct-gtatttctaaggatgaatagccaatcattgagtgttacggttaccagATTGCAGATGTATGGTCATGTGGTGTGACCTTATACGTCATGTTGGTTGGAGCGTATCCGTTCGAAGATCCAGAAGAGCCAAGAGACTATCGGAAAACAA
| | |||| | | |||| || | || | || | | | | || | || | | | |||||||| ||||| ||||| || |||||||| || ||||| |||||||| ||||||||||| || || ||||| ||||| ||||| | | | ||||| |
gtgagttcgtcggacgataacttagttgtattggtatggagtagtcccggcgttgtattgttagtttttccaagtagacgctgttgtcgatagtgtcggtatcggtcagctgagaagacagaaatgctttgatatgcagATTGCCGATGTTTGGTCGTGCGGTGTGACTTTGTACGTGATGTTGGTCGGAGCGTATCCCTTTGAGGATCCCGAAGATCCAAGGAATTTCAGAAAAACTA
upper sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: PP1S116_98V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------------------gtaaaggcttttagagaattcctctgtaatctctgtatttctaaggatgaatagccaatcattgagtgttacggttaccagATTGCAGATGTATGGTCATGTGGTGTGACCTTATACGTCATGTTGGTTGGAGCGTATCCGTTCGAAGATCCAGAAGAGCCAAGAGACTATCGGAAAACAA
| ||| | |||| | | || | | | || | ||| | || | || |||||||| ||||| ||||| || ||||||||||| |||||||||||||| ||||| || || ||||| ||||| | || ||||| | | ||||||| |
gtacgtggtttgcacaagggtttttgaccgcaaggattggggtttcgcttcatgatgtctttctactgaatcaagtgtgttagtg---tttactaaagttcaaggcaccttatcggggaactgaaggaacccacttgcttcgagatgcagATTGCGGATGTGTGGTCGTGCGGTGTGACCTTGTACGTCATGTTGGTGGGAGCATACCCATTCGAGGATCCCTATGACCCAAGGAATTTCAGGAAAACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatctctgtatttctaaggatgaatagccaatcattgagtgttacggttaccagATTGCAGATGTATGGTCATGTGGTGTGACCTTATACGTCATGTTGGTTGGAGCGTATCCGTTCGAAGATCCAGAAGAGCCAAGAGACTATCGGAAAACAA
tatttctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaggcttttagagaattcctctgtaatctctgtatttctaaggatgaatagccaatcattgagtgttacggttaccagATTGCAGATGTATGGTCATGTGGTGTGACCTTATACGTCATGTTGGTTGGAGCGTATCCGTTCGAAGATCCAGAAGAGCCAAGAGACTATCGGAAAACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA