Sequence
atgc intronic sequence ATGC exonic sequencegttagattcttttaaataacacgaacatattcattcagttgcattcaaacacaaattatattgatgttatattaatttggttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G27150.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
gttagatt---cttttaaataacacgaacatattcattcagttgcattc-aaacacaaattatattgatgttatattaatt--tggttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA
|| | | |||| | | | || || | ||| |||| |||| | | ||| ||| | || | || || | | |||| | | || |||||||| || ||||| || || |||||||||||||| ||||| |||||||| ||||| || || || ||||| |||||| | |||||||
gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcattttatagtttgattttatctactttgt-ttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
upper sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os11g42790.1 (Oryza sativa), 3'ss of exon 7
----------------gttagattcttttaaataacacgaacatattcat--tcagttgcattcaaacacaaattata--ttgatgttatatta----atttggttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA
|||| || | || || | | | || |||| | ||| || || ||| |||| ||| | ||| || |||| | | || ||||| ||||| || || ||||| |||||||||||||| ||||| || || || ||||| |||||||| ||||| || || | ||||| |
gtaagcaccctgtactattagcatcatatagatcctgcagatttgagcaatgtcagctaaatttaattgtaatggataatctgatattaacctgtttctttttgtggcagTTGCTTGATTTGAGTGGTATTCTTACGGTGTTCTTCTGTGGTATTGTAATGTCGCACTATACCTGGCATAATGTAACAGAGAGTTCCAGGGTCACAACCA
upper sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G311165_T01 (Zea mays), 3'ss of exon 8
------gttagattcttttaaataacacgaacatattcattcagttgcattcaaacacaaat-tatattgatgtta------tattaatttggttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA
| ||||||| | |||| || | || | |||||| | | || |||| | ||| | | ||| | || | |||| ||||| || || ||||||||||||||||||||||| || ||||| || || || ||||| |||||||| || || || || | ||||| |
gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgtaagTTGCTCGATTTGAGTGGCATTCTCACTGTGTTTTTCTGTGGTATCGTAATGTCACACTATACTTGGCAAAATGTAACAGAAAGTTCGAGGGTCACAACCA
upper sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G311165_T06 (Zea mays), 3'ss of exon 7
------gttagattcttttaaataacacgaacatattcattcagttgcattcaaacacaaat-tatattgatgtta------tattaatttggttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA-
| ||||||| | |||| || | || | |||||| | | || |||| | ||| | | ||| | || | |||| ||||| || || ||||||||||||||||||||||| || ||||| || || || ||||| |||||||| || || || || | ||||| |
gtgagcaccctgtacttttaacctctgcagacattttgcattttttaaaagcaaacatagctgtaaattgttattaacgggttgcttttttattgtaagttgctcgatttgagtggcattctcactgtgtttttctgtggtatcgtaatgtcacactatacttggcaaaatgtaacagAAAGTTCGAGGGTCACAACCAA
upper sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 6
gttagattctt-ttaaataacacgaacatattcattca-gttgcatt-caaacacaaattatattgatgttatattaatttggttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA
|| ||| | | || | | ||||| | |||| || | | || | | || | ||||| | |||||||| | || |||| || || || || || || ||||| || || |||||||| |||||||| ||||||||||| || |||||||||||| | ||||| |
gtgcacctctgatcagatgtggcaagggaattcacgcttgttgtcttactctcttaactgactctgttcatatat-atggcatttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATGTCGCATTACACCTGGCACAATGTGACAGAGAGCTCAAGAGTCACAACCA
upper sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------------------------gttagattcttttaaata-----------acacgaacatattcattcagttg------cattcaaacacaaa--ttatattgatgttatattaatttg--------gttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA
| || | ||| ||||| | | || |||| || ||| | | ||| || || | || ||| || || | ||||||||||| ||||||| || || ||| | ||||| || ||||| ||||| ||||| |||||||| ||||| ||||| ||||| | || ||| ||||| |
gtcagtttgaccttctatgtggattgttcgtccaattatctgttcctggaatttttcaaatagatcgatgaggaaatgagcatacgatttggattgttacaacttgtaaatctgaaattttcagaaattttactttcgcgtgtcgtcattggtgcagCTTTTCTACTTGAGTGGAATACTCTCAGTGTTCTTTTGTGGCATTGTAATGTCTCATTACACTTGGCATAATGTCACGGAAAATTCTCGAACCACAACCA
upper sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ05720 (Selaginella moellendorffii), 3'ss of exon 7
gttagattcttttaaataacacgaacatattcattcagttgcattcaaacacaaattatattgatgttatattaatttggttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA
| | || ||| || || | | ||| | | || || || ||||| ||| || |||| || |||||||| || || || ||||| ||||| ||||| ||||| ||||||||||| || ||||||||||||||||| ||||| |
---------------------gtgatagtttttttctgtatagagaggtagcatttcttcttgttctcatgcgtatgccattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA
upper sequence: AT5G27150.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ32893 (Selaginella moellendorffii), 3'ss of exon 7
gttagattcttttaaataacacgaacatattcattcagttgcattcaaacacaaattatattgatgttatattaatttggttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA
|| | || ||| || || | | ||| | | || || || ||||| ||| || |||| || |||||||| || || || ||||| ||||| ||||| ||||| ||||||||||| || ||||||||||||||||| ||||| |
--------------------gtgagagt-ttttttctgtatagagaggtagcatttcttcttgttctcatgcgtatgccattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattcagttgcattcaaacacaaattatattgatgttatattaatttggttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA
tattaat putative branch site (score: 2)
attcaaacacaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagattcttttaaataacacgaacatattcattcagttgcattcaaacacaaattatattgatgttatattaatttggttgcagCTTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA