Sequence
atgc intronic sequence ATGC exonic sequencegttcacccatacttctttaactttcttctatctgtttgtttttcctgttattaccgtaacataaccattgtgtttttcagAGAAACAAAGCACCATATGAGGATTCAATTCCGCTTCTTATGCCTCAACATCACATGGTTATACCCCACTACATGGGAAGGCAAGAGGAGTCAGACATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G16785.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os01g20860.1 (Oryza sativa), 3'ss of exon 9
gttcacccatacttctttaactttcttctatctgtttgtttttcctgttattaccgtaacataaccatt--gtgtttttcagAGAAACAAAGCACCATATGAGGATTCAATTCCGCTTCTTATGCCTCAACATCACATGGTTATACCCCACTACATGGGAAGGCAAGAGGAGTCAGACATTG
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---------------gtatgtttactggttaatattactcatccctatcaccgttgaaat-tgacaactcaatcttatgcagAGGAACAAAGCACCAAATGAGCAAGCAATTCCCTTATTGATGCCTCAACATCACATGGTAATTCCCCATTACATGGGTAAAATCAAAGAATCAAATGAGG
upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 11
----------------gttcacccatacttctttaactttcttctatctgtttgtttttcctgttattaccgtaacataaccattgtgtt--tttcagAGAAACAAAGCACCATATGAGGATTCAATTCCGCTTCTTATGCCTCAACATCACATGGTTATACCCCACTACATGGGAAGGCAAGAGGAGTCAGACATTG
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gttagtcttattttgcagttgcattgaagtcttgaagcattctggtcctattcctatattcccaaaataggaaataatattttttttattaacatcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 11
----------------gttcacccatacttctttaactttcttctatctgtttgtttttcctgttattaccgtaacataaccattgtgtt--tttcagAGAAACAAAGCACCATATGAGGATTCAATTCCGCTTCTTATGCCTCAACATCACATGGTTATACCCCACTACATGGGAAGGCAAGAGGAGTCAGACATTG
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gttagtcttattttgcaattgcattgaagtcttggagcattctggtcctattcctatattccctaaataggaaataatattttttttattaacgtcagAGGAACAAAGCTCCATATGAGCAAGCAATTCCATTACTTATGCCTCAGCATCATATGGTTATTCCACATTACTTGGGAAGAAGCAGAGAGATACAGATTG
upper sequence: AT3G16785.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 12
--------gttcacc-catacttctttaactttcttctatctgtttgtttttcctgttattaccgtaacataaccattgtgtttttcagAGAAACAAAGCACCATATGAGGATTCAATTCCGCTTCTTATGCCTCAACATCACATGGTTATACCCCACTACATGGGAAGGCAAGAGGAGTCAGACATTG
||||| |||||| | | ||||| | || | | ||| |||| | || | || ||| | || | |||||||| ||||| ||| ||||| | ||||||| || ||||||||||| || |||||||| || || || |||||||||||| ||| || |||
gttgatgtcttcactacatactccctagttcttctttcaaaagtataataaaccttttat---ctcaatacaagcatacttttctgcagAGAAATAAAGCTCCAAATGAGCAAGCAATTCCACTACTTATGCCTCAGCAGCACATGGTCATTCCACATTACATGGGAAGGAGCAGAGAGATGGAGGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctatctgtttgtttttcctgttattaccgtaacataaccattgtgtttttcagAGAAACAAAGCACCATATGAGGATTCAATTCCGCTTCTTATGCCTCAACATCACATGGTTATACCCCACTACATGGGAAGGCAAGAGGAGTCAGACATTG
acataac putative branch site (score: 3)
tgtttttc putative PPT
tttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcacccatacttctttaactttcttctatctgtttgtttttcctgttattaccgtaacataaccattgtgtttttcagAGAAACAAAGCACCATATGAGGATTCAATTCCGCTTCTTATGCCTCAACATCACATGGTTATACCCCACTACATGGGAAGGCAAGAGGAGTCAGACATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG