Sequence
atgc intronic sequence ATGC exonic sequencegttagtgttggttacttttctggcaagaaagctgaaaccctaaatgattctctattgattctatcataagctggttttactttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16340.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: LOC_Os06g36090.2 (Oryza sativa), 3'ss of exon 17
gttagtgttggttacttttctggcaagaaagc------tgaaaccctaaatgattctctattgattctatcataagctggttttactttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA
|| | |||||| | | ||| | | ||| | || |||| ||| | | | | || | || | | | || ||||| ||||| ||||||||||| ||||| |||||| | || ||| |||| ||||| |||||||| | || || | ||||| || ||| | || | | |
----------gtgagttttcttggatcaaaccgtttctttgaactttttattcttcttggaagatcaaagta-atggtgttattcatgttttatttcagAGGATTCCCAAATGGTGGATCTGGTACTACTGGCTTTGCCCATTGGCATGGACAGTGTATGGGCTCATAGTGACACAGTATGGAGACCTAGAACAAATCA
upper sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G366146_T01 (Zea mays), 3'ss of exon 17
gttagtgttggttacttttctgg-caagaaagctgaaaccctaaatgattctctattgattctatcataagctggttttact---ttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA
||| ||| || | || | | | ||| | | | | | || | || |||| || ||| | || ||||||||||| | ||||||||| ||||| |||||||| || ||| |||| ||||| |||||||| | || || | || ||||| ||| || | || | |
------gttagttgtttcttcaatcacctttaccgtgatccttttctgtaggattaaaaataatgcttatgttgttttttctctattcttatttcagAGAATTCCTAGATGGTGGATCTGGTACTACTGGATTTGCCCATTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGCAAGACCCCA
upper sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GRMZM2G029506_T01 (Zea mays), 3'ss of exon 21
gttagtgttggttact-tttctggcaagaaagctgaaaccctaaatgattctctattgattctatcataagct---ggttttact---ttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA
|| ||| | |||| || | ||| | ||| || || |||| || || | |||| || ||||| || ||||||||||| ||||||||| ||||| |||||||| || ||| |||| ||||| |||||||| | || || | || ||||| ||| |||| || |
------gtcagttgttgtttcaatcaccatccctgcgatccttttcctacctgtag-gattaaatagaggactcatgttttttctctattcctgtttcagAGAATTCCTGGATGGTGGATCTGGTACTACTGGATTTGCCCACTGGCATGGACAGTGTATGGGCTCATCGTGACACAATACGGAGACCTGGAAGACCTCA
upper sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA08G21540.1 (Glycine max), 3'ss of exon 21
gttagtgttggttacttttctggcaagaaagctgaaaccctaaatgattctctattgattctatcataagctggtttt---actttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA
|| ||| | |||| | || |||||| | || | || || | || || | | ||||| || |||| |||||| ||||||||| | |||||||||||||| ||||||||||| ||||| ||||||||||| ||||| || || || | || | ||||| |
gtgagtaccattccagtttc--gtaattttattgaaaca--agcatatcttacataatccttactaaaaactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCCAC
upper sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA07G01860.1 (Glycine max), 3'ss of exon 22
gttagtgttggttacttttctggcaagaaagctgaaaccc-taaatgattctctattgattctatcataagctggtt--ttactttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA
|| ||| | |||| | | | |||||| | || | | || | ||| ||||| | ||||| || |||| |||||| ||||||||| | |||||||||||||| ||||||||||| ||||| ||||||||||| ||||| || || || | || | |||||
gtgagtaccattctaatttc--gttattatattgaaacaaacatatcttacataatctttactaacataactcttctaccaactttggcttttcagAAAATTCCTAAATGGTGGGTGTGGTATTACTGGATTTGTCCAGTGGCATGGACAGTGTATGGATTAATTGTCTCTCAATATAGAGATATAGAGGACCATC
upper sequence: AT3G16340.1 (Arabidopsis thaliana), 3'ss of exon 18
lower sequence: GLYMA13G43140.1 (Glycine max), 3'ss of exon 21
gttagtgttggttacttttctggcaagaa--agctga---aaccctaaatga----ttct--ctattgattctatcataag--ctggttttactttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA
|| || || | ||||| |||| | | | |||| || |||| ||| |||| ||||| || | ||||| || |||| |||||| ||||||||| | |||||||| ||||| || ||||| || |||||||||||||| || ||||| || || || || || || ||| ||
------aatgactaaattgataaaaagaaatagcttatttagcaataaaagaattattcttgtcattttctctaacataattcctctatcaactttgacatttcagAAAATTCCTAAATGGTGGGTTTGGTATTATTGGATTTGCCCAGTAGCGTGGACTGTGTATGGGTTAATTGTCTCACAATATGGAGATGTAGAGATAGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctaaatgattctctattgattctatcataagctggttttactttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA
tattgat putative branch site (score: 3)
ttttactttcctcttg putative PPT
ttttacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgttggttacttttctggcaagaaagctgaaaccctaaatgattctctattgattctatcataagctggttttactttcctcttgcagAGAATTCCGAAATGGTGGATATGGTATTACTGGATCTGTCCAGTGGCTTGGACTGTGTATGGATTGATTGTTTCGCAGTACGGTGACGTGGAGGATACGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT