Sequence
atgc intronic sequence ATGC exonic sequence...ctagctacatgtttgtttcgtctcaaagattatattgattcgaactttcgttttccttaacatgaactcatcacaatgtttatgaacttttgaactgcagTCAGAATGGAAAATTTAGCTATGGATATGCAAGCTCAGCTGGAAAAAGGTCATCTATGGAAGACTTTTTTGAGACAAGGATCGACGGTATCGATGGAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G24940.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G24940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os04g56450.1 (Oryza sativa), 3'ss of exon 1
-----ctagctacatgtttgtttcgtctcaaag----attatattgattcgaactttcgttttccttaacatgaactcatcacaatgtttatgaacttttgaactgcagTCAGAATGGAAAATTTAGCTATGGATATGCAAGCTCAGCTGGAAAAAGGTCATCTATGGAAGACTTTTTTGAGACAAGGATCGACGGTATCGATGGAGAA
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aatcaacgttgtcatggtagcttgattttatggtgtaaatgcagttattaggactgttgctctcct----atttgctcaaca-----tttctcattctttttttgccagCCAGAATGGTAAGTTTAGCTATGGGTATGCGAGCTCCCCTGGTAAAAGGGCTTCCATGGAAGACTTTTACGAGACAAGAATTGACTCTGTTGATGGGCAG
upper sequence: AT5G24940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os06g48300.1 (Oryza sativa), 3'ss of exon 1
ctagctacatgtttgtttcgtctcaaagattatattgattc---gaactttcgttttccttaacatgaactcatcacaatgtttatgaacttttga-actgcagTCAGAATGGAAAATTTAGCTATGGATATGCAAGCTCAGCTGGAAAAAGGTCATCTATGGAAGACTTTTTTGAGACAAGGATCGACGGTATCGATGGAGAA
|||| |||||| | | |||| ||| || ||||||| ||| || | || || |||| | | || | |||| ||||| |||||||||||||| ||||| ||||| |||||||||| || || ||||| ||||| | ||| || || || || ||| ||||||||||
----gggagtgttagtttcgaatatctgtatatagccattgacagagaattcgtttctgttattattacctgatattgttgttcttcttgtgttatcatgacagTGCAAATGGTAAATTTAGCTATGGTTATGCGAGCTCTCCTGGAAAAAGATCCTCCATGGAGGACTTCTATGACACCAGAATTGATGGTGTCGATGGAGAG
upper sequence: AT5G24940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 1
ctagctacatgtttgtttcgtctcaaagattatattgattcgaactttcgt-tttccttaacatgaactcatca--caatgttt-atgaacttttgaactgc-agTCAGAATGGAAAATTTAGCTATGGATATGCAAGCTCAGCTGGAAAAAGGTCATCTATGGAAGACTTTTTTGAGACAAGGATCGACGGTATCGATGGAGAA
| | |||| | | || | |||| || | || | | ||| || | || | || | || | || ||||| | ||| |||| || |||||||| | |||||||||||| ||||||||||| |||| |||||| |||| ||||||||||| | |||||||| || || || | ||||| |
-ttgttacag--tagcttggctccaaatatcaaatcagt--ggactatcatgttgttcttgtattacctatttgttcagtgtttcacatttattttttctgccagCCAGAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAG
upper sequence: AT5G24940.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G056572_T01 (Zea mays), 3'ss of exon 1
ctagctacatgtttgtttcgtctcaaagattatattgattcgaactttcgt-tttccttaacatgaactcatca--caatgttt-atgaacttttgaactgc-agTCAGAATGGAAAATTTAGCTATGGATATGCAAGCTCAGCTGGAAAAAGGTCATCTATGGAAGACTTTTTTGAGACAAGGATCGACGGTATCGATGGAGAA----
| | | || | |||| || | || | | ||| || | || | || | || | || ||||| | ||| |||| || |||||||| | |||||||||||| ||||||||||| |||| |||||| |||| ||||||||||| | |||||||| || || || | ||||| |
-------tacagtagcttggctccaaatatcaaatcagt--ggactatcatgttgttcttgtattacctatttgttcagtgtttcacatttattttttctgccagccagAATGGTAGATTTAGCTATGGCTATGCAAGCTCCCCTGGTAAAAGGGCATCCATGGAAGACTTCTATGAGACAAAAATTGATTGTGTTGATGGTCAGATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcgttttccttaacatgaactcatcacaatgtttatgaacttttgaactgcagTCAGAATGGAAAATTTAGCTATGGATATGCAAGCTCAGCTGGAAAAAGGTCATCTATGGAAGACTTTTTTGAGACAAGGATCGACGGTATCGATGGAGAA
ccttaac putative branch site (score: 3)
ctttt putative PPT
aatgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctagctacatgtttgtttcgtctcaaagattatattgattcgaactttcgttttccttaacatgaactcatcacaatgtttatgaacttttgaactgcagTCAGAATGGAAAATTTAGCTATGGATATGCAAGCTCAGCTGGAAAAAGGTCATCTATGGAAGACTTTTTTGAGACAAGGATCGACGGTATCGATGGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - -tgtttgt
- - - - - - - - - - tctcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catcaca