Sequence
atgc intronic sequence ATGC exonic sequencegtacttcccaaactttccccctaatgaatcaatgcaaaattgttgacaaaaaatagtatcaagaccaaactctcaagtttgacttcttgtttgttttctccattcctcatgaagttagttttaccccacagAACTTTTCCAGAGATTATTCAGACAGGACTTGTTGGTTGCTAGCCTTTTCCGAAATTTCTTACTAGCTGAGAGGATAATGCGGTCCGGAAATTGTACCCC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01770.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 6
gtacttcccaaactttccccctaatgaatcaatgcaaaattgttgacaaaaaatagtatcaagaccaaactctcaagtttgacttcttgtttgttttctcc--attcctcatgaagttagttttaccccacagAACTTTTCCAGAGATTATTCAGACAGGACTTGTTGGTTGCTAGCCTTTTCCGAAATTTCTTACTAGCTGAGAGGATAATGCGGTCCGGAAATTGTACCCC
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---------------------------------gtactgatagtcattttaatcacaattaatgccag-tgatcaa--ttgctttctcattcattttcttttaatctgttatgattcaactttcactacgcagATCTATTCCAAAGACTTTTCAGGCAGGATCTTTTGGTTGCTAGTCTCTTTCGCAACTTCTTACTTGCTGAGAGAATCATGCGGTCCGCAAATTGTTCCCC
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 7
gtacttcccaaactttccccctaatgaatcaatgcaaaattgttgacaaaaaatagtatcaagaccaaactctcaagtttgacttcttgtttgttttctcc--attcctcatgaagttagttttaccccacagAACTTTTCCAGAGATTATTCAGACAGGACTTGTTGGTTGCTAGCCTTTTCCGAAATTTCTTACTAGCTGAGAGGATAATGCGGTCCGGAAATTGTACCCC
| | | | | || || || ||| |||| ||| |||| || |||||| || | |||| | ||| || | |||| || ||||| ||| | ||||| ||||| | ||||||||||| || || || || |||||||| |||||||| || |||||||||| ||||||| ||||
---------------------------------gtactgatagtcgttttagttacaattaatgccag-tgatcaa--ttgctttctcattcattttcttttaatctgttatgattcaactttcactgcgcagATCTATTCCAAAGACTTTTCAGGCAGGATCTTTTGGTTGCTAGTCTCTTTCGCAACTTCTTACTTGCTGAGAGAATCATGCGGTCCGCAAATTGTTCCCC
upper sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 7
gtacttcccaaactttccccctaatgaatcaatgcaaaattgttgacaaaaaatagtatcaagaccaaactctcaagtttg-acttcttgtttgttttctcca---ttcctcatgaa-gttagttttaccccacagAACTTTTCCAGAGATTATTCAGACAGGACTTGTTGGTTGCTAGCCTTTTCCGAAATTTCTTACTAGCTGAGAGGATAATGCGGTCCGGAAATTGTACCCC
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-----------------------gtaatttaat--tggcttactgattttatgcagcatgagcaatcagctgttaaatttttaatttgtttttattctccttacggtggtatatgcatatttattttgtgctgcagATCTTTTTCAGAGATTGTTCAGGCAAGACCTGTTAGTTGCCAGTCTGTTTCGAAATTTCTTACTTGCTGAGAGAATTATGCGATCTGCAAACTGTTCCCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgacttcttgtttgttttctccattcctcatgaagttagttttaccccacagAACTTTTCCAGAGATTATTCAGACAGGACTTGTTGGTTGCTAGCCTTTTCCGAAATTTCTTACTAGCTGAGAGGATAATGCGGTCCGGAAATTGTACCCC
gtttgac putative branch site (score: 4)
ttttacccc putative PPT
ttagtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttcccaaactttccccctaatgaatcaatgcaaaattgttgacaaaaaatagtatcaagaccaaactctcaagtttgacttcttgtttgttttctccattcctcatgaagttagttttaccccacagAACTTTTCCAGAGATTATTCAGACAGGACTTGTTGGTTGCTAGCCTTTTCCGAAATTTCTTACTAGCTGAGAGGATAATGCGGTCCGGAAATTGTACCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT