Sequence
atgc intronic sequence ATGC exonic sequencegtaatcaatctccttaaaagaatgcaagtttgagtcttttgatatagaaactaagtcaatggcttttttcggttgacagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G56500.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 12
--gtaatcaatctccttaaaagaatgcaagtttgagtcttttgatatagaaactaagtcaatggcttttttcggttgacagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA
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gttagatcttgttcactaacagaaaatca-tatgttcacatgtacatctgaataacataaaagatgatgtt---ttaccagGTTCTCTCTAACGATAACTTCAAGTTTGGTTACAATGCTGCAACTGGACAGTACGAGGATTTGATGGCTGCTGGTATCATTGACCCCACTAAG
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 12
--gtaatcaatctccttaaaagaatgcaa--gtttgagtcttttgatatagaaac--taagtcaatggcttttttcggttgacagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA
|||||||| || | || | | | | || | |||| || | | | ||||| ||| ||||| || || |||||||| || ||| |||| | |||||||||||| || ||||| |||||||| |||||||| ||||| ||||| || || ||
gtataatcaatgagtttccaggaggtccatgatctctgtttcatgatgtatatgtgttgaccaaatgggagctttt-----tcagGTGCTCTCCAGTGACAATCCAAAATATGGGTTCAATGCTGCAACAGGAAAATATGAAGATCTAATGGCTGCTGGAATAATTGACCCTACTAAG
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ36935 (Selaginella moellendorffii), 3'ss of exon 11
gtaatcaatctccttaaaagaatgcaagtttgagtcttttgatatagaaactaagtcaatggcttttttcggttg---acagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA
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-----------------------------gtaagactttctacctgcggcttggcttgagttttgactgccggtgtgtgcagGTCCTTGCCGACGATAACTTTAACCACGGTTATAATGCTGCGACTGGTGCATTTGAGAATCTCATGGCGGCAGGAATCATTGATCCAACCAAG
upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ33580 (Selaginella moellendorffii), 3'ss of exon 11
gtaatcaatctccttaaaagaatgcaagtttgagtcttttgatatagaaactaagtcaatggcttttttcggttgacagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA
| | |||| || | | | ||| || || | || ||||| ||| | || ||| ||| || ||||| |||||||| ||||| || || |||||||||| |||||||||||||||||||||||
---------------------gtaagactttgtacctgcggctt---ggcttgagttt-tgactgccggtgtgtg-cagGTCCTTGCCGACGATAACTTTAACCACGGTTATAATGCTGCGACTGGTGCATTTGAGAATCTCATGGCGGCAGGAATCATTGATCCAACCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caagtttgagtcttttgatatagaaactaagtcaatggcttttttcggttgacagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA
ttttgat putative branch site (score: 4)
cttttttc putative PPT
ttttgatatagaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatcaatctccttaaaagaatgcaagtttgagtcttttgatatagaaactaagtcaatggcttttttcggttgacagGTTCTTTCTAGTGACAACCCTAAACATGGTTACAATGCTGCAACTGGCAAATACGAAGATCTCATGGCTGCAGGAATCATTGATCCAACCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG