Sequence
atgc intronic sequence ATGC exonic sequencegtgcgttttaatcattctctaattgttttttttcgtttatcgatttgtttgatgaagctgattcgatgaacttgtattagGTTTCGATTGCTAGAACTTGCAATTGCGTATACGCTTTGATTCAACAGAGGCAACGAGATGTGGAATTTAGAGAATCTGCTAATGATCAGAGACAACG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G18876.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G18876.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 3
----------------------------gtgcgttttaatcattctcta-attgttttttttcgtttatcgatttgtttgatgaagctgattcgatgaacttgtattagGTTTCGATTGCTAGAACTTGCAATTGCGTATACGCTTTGATTCAACAGAGGCAACGAGATGTGGAATTTAGAGAATCTGCTAATGATCAGAGACAACG
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gtgagtattgaactgatcccgttccgtctttcatgtgcattgttttttgcgccaatgtatgtagtatgcacattatgtgaatgatgctgttttgaaaaa--tgtggtagGTTTCAATTGCGAGGACTTGCAATTGCATTTACGTCTTGCTGCAGCAGAGACAGCGCGACGTGGAGTTTAGAGAGTCTGCTAATGATCAAAGACAACG
upper sequence: AT2G18876.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 3
-----------------------gtgcgttttaatcattctctaattgttttttttcgtttatcgatttgtttgatgaagctgattcgat----gaacttgtattagGTTTCGATTGCTAGAACTTGCAATTGCGTATACGCTTTGATTCAACAGAGGCAACGAGATGTGGAATTTAGAGAATCTGCTAATGATCAGAGACAACG
|| ||| | | | | | | |||| | | | ||| | ||| |||| | ||| ||| |||||||| ||||| || |||||||||||| | ||| ||| | || ||||| || || || || ||||||||||| |||||||||||||| ||||||||
gtgagaattgaactgatcccgttctgtctttcatttacattgttttgtttttcgccaatgtgtgagcgtgtgttatgtgaatgatgttgttctggaaaatgtggtagGTTTCAATTGCGAGGACTTGCAATTGCATTTACTTCTTGCTCCAGCAGAGACAGCGCGACGTTGAATTTAGAGAGTCTGCTAATGATCAAAGACAACG
upper sequence: AT2G18876.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 3
gtgcgttttaatcattctctaattgttttttttcgtttatcgatttg---tttgatgaagctgattcgatgaacttg-tattagGTTTCGATTGCTAGAACTTGCAATTGCGTATACGCTTTGATTCAACAGAGGCAACGAGATGTGGAATTTAGAGAATCTGCTAATGATCAGAGACAACG
||||| | | || |||||||| | | |||| || | | |||||| | || | ||| | |||||||||||||| | || || |||||| | ||| || || | || |||||||| || ||||| |||||||| || ||||||||||| |||||||| ||
gtgcggagtggttgtttgtggattgttttgtgtggttttgggagtggggttttgattgttgcgtttttgcgcttttggtggtagGTTTCGATTGCGCGGACCTGTAATTGCATTTACTCTCTGCTGCAGCAGAGGCAGCGTGATGTTGAATTTAGGGAGTCTGCTAATGAGCAGAGACAGCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttttcgtttatcgatttgtttgatgaagctgattcgatgaacttgtattagGTTTCGATTGCTAGAACTTGCAATTGCGTATACGCTTTGATTCAACAGAGGCAACGAGATGTGGAATTTAGAGAATCTGCTAATGATCAGAGACAACG
agctgat putative branch site (score: 4)
atttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcgttttaatcattctctaattgttttttttcgtttatcgatttgtttgatgaagctgattcgatgaacttgtattagGTTTCGATTGCTAGAACTTGCAATTGCGTATACGCTTTGATTCAACAGAGGCAACGAGATGTGGAATTTAGAGAATCTGCTAATGATCAGAGACAACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG