Sequence
atgc intronic sequence ATGC exonic sequencegtatgtagaagcctttctttttacccgttttgagttggtttttccctataacaggaactaaccagtatcgaacttttgtgtcattcaaaaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G67850.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 5
gtatgtagaagcctttctttttacccgttttgagttggtttttccctataacaggaactaaccagtatcgaacttttgtgt----cattcaaaaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG
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ttgagcagtactgttgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0106g00570.t01 (Vitis vinifera), 3'ss of exon 1
------------gtatgtagaagcctttctttttacccgttttgagttggtttttccctataacaggaactaaccagtatcgaacttttgtgt----cattcaaaaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG
| | | | || | ||| | || | | | | || | || | | || || | || | || |||||||| || || ||||||||||||||||||||||| ||| |||| ||||| || ||||||||| || | |||
gtatgaaaagctttgagcaatactattgttattttttctgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagttttccttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 10
gtatgtaga------agcctttctttttacccgttttgagttggtttttccctataacagg------aactaaccagtatcgaacttttgtgtcattcaa----aaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG
||||| | | ||| | || || ||||| ||| || | | || || | || | | || || | || ||| |||||||| || || ||||||||||||||||||||||| ||| |||| ||||| || ||||||||| || | |||
gtatgaaaagctttgagcagtactattgttattttttgtgttcattcccactcctgcatggtctgacaatggattagaaacaaaattattagtttttcttttccaaatgcagGTTTGTTGAGATCATGGCTCCTGTATTTTCTAGAGATGCATGGCGGTGTGTGTGGCATATGCTTCAG
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
---------------gtatgtag--aagcctttctttttacccgttttgagttggtttttccctataacaggaactaaccagtatcgaacttttgtgtcattcaaaaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG
|||| ||| | || | | | || | | ||||| || | || | | | || | | || | | || || | |||||||| || ||||||||||||||||| |||||| |||| || ||||| ||| | ||| | | || |||
gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggtatttacttcttgtttaatactgcagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ06933 (Selaginella moellendorffii), 3'ss of exon 9
gtatgtagaagcctttctttttacccgttttgagttggtttttccctataacaggaactaaccagtatcgaacttttgtgtcattcaaaaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG---------------------------------
|| || || | | | ||| || | | || ||| || ||||||| || |||||||||||||| || ||||| || ||||| ||| |||||||||||||| |||| ||
---------------------------------gtaagtcttggctttcacttggacatag--atttctatttcttagtggtgtttctg---gcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC
upper sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ09147 (Selaginella moellendorffii), 3'ss of exon 6
gtatgtagaagcctttctttttacccgttttgagttggtttttccctataacaggaactaaccagtatcgaacttttgtgtcattcaaaaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG---------------------------------
|| || || | | | ||| || | | || |||| || ||||||| || |||||||||||||| || ||||| || ||||| ||| |||||||||||||| |||| ||
---------------------------------gtaagtcttggctttcacttggacatag--atttctatttcttagtgttgtttctg---gcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccctataacaggaactaaccagtatcgaacttttgtgtcattcaaaaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG
aactaac putative branch site (score: 1)
attcaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtagaagcctttctttttacccgttttgagttggtttttccctataacaggaactaaccagtatcgaacttttgtgtcattcaaaaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA