Sequence
atgc intronic sequence ATGC exonic sequence...cagctcaaggtttgagtctcgcctttttgttttcagaatgttgaatgttggcttcttacggtaaaatcgagtttgattctaatacgtatatcgtgtatagGCTGCTGAACCATTCTTCTTGTTGGCTGGTCCAAATGTGATTGAATCCGAGGAACATATTCTTCGAATGGCAAAGCACATTAAAGACATTTCCACAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G79500.5 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G79500.5 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os12g10784.3 (Oryza sativa), 3'ss of exon 2
-------cagctcaaggtttgagtctcgcctttttgttttcagaatgttgaatgttggct-tcttacggtaaaatcgagtttgattctaatacgtatatcgtgtatagGCTGCTGAACCATTCTTCTTGTTGGCTGGTCCAAATGTGATTGAATCCGAGGAACATATTCTTCGAATGGCAAAGCACATTAAAGACATTTCCACAAA
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aaatatactattggtgtgatcacattcaatgcctggttttatttagaggaaacacaggttatttttctgtgagaactgaacc--ctctgattcttaca------acagGCTGCTCAACCATTCTTCTTGTTAGCTGGGCCTAATGTGATTGAATCAGAGGAGCATGTCCTGAAGATGGCAAAACACATCAAAGGCATCACAACCAA
upper sequence: AT1G79500.5 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G168510_T02 (Zea mays), 3'ss of exon 2
cagctcaaggtttgagtctcgcctttttgttttcagaatgttgaatgttggcttcttacggta-aaatcgagtttgattctaata-cgtatatcgtgta-tagGCTGCTGAACCATTCTTCTTGTTGGCTGGTCCAAATGTGATTGAATCCGAGGAACATATTCTTCGAATGGCAAAGCACATTAAAGACATTTCCACAAA
|| | || ||| | | || | | || | | | ||| || | || | | || | || || | | || || | |||| || |||| |||||||||||||||||||| || ||||||||||| ||||| || | || ||||| || ||||| |||| ||| | || ||
-agtttcttcgtttgccctcacatgaatgatat--aaacgacaacttttgtgatcatgtattatgtactgtgtgtttttttatcaatctgattcttgcaacagGCAGCCAAACCGTTCTTCTTGTTGGCTGGTCCCAACGTGATTGAATCGGAGGAGCACGTCCTGAAGATGGCCAAACACATCAAAGCAATTACGACCAA
upper sequence: AT1G79500.5 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0085g00720.t01 (Vitis vinifera), 3'ss of exon 1
---cagctcaaggtttgagtctcgcctttttgttttcagaatgttgaatgtt-ggcttcttacggtaaaatcgagtttgatt-ctaatacg-tatatcgtgtatagGCTGCTGAACCATTCTTCTTGTTGGCTGGTCCAAATGTGATTGAATCCGAGGAACATATTCTTCGAATGGCAAAGCACATTAAAGACATTTCCACAAA
| ||| ||| || | | |||| |||| | |||| | || | || | | | | ||| |||| ||| || | | | || | | || | | ||||| || ||||||||||||||||| |||||||||||||| ||||| || ||| | ||||| || ||| || | | ||||
gtttggatca--ctttatgtttttctttttctttttt----tattgattttttgaattgtaatgatttaatattgtttaattgctgtgatgatttactgaaaacagTCATCAGAACCCTTTTTCTTGTTGGCTGGTCCCAATGTGATTGAATCTGAGGAGCACATTATGTATATGGCCAAAGCCATCAAGAGTCTCACATCAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttggcttcttacggtaaaatcgagtttgattctaatacgtatatcgtgtatagGCTGCTGAACCATTCTTCTTGTTGGCTGGTCCAAATGTGATTGAATCCGAGGAACATATTCTTCGAATGGCAAAGCACATTAAAGACATTTCCACAAA
ttctaat putative branch site (score: 2)
attctaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagctcaaggtttgagtctcgcctttttgttttcagaatgttgaatgttggcttcttacggtaaaatcgagtttgattctaatacgtatatcgtgtatagGCTGCTGAACCATTCTTCTTGTTGGCTGGTCCAAATGTGATTGAATCCGAGGAACATATTCTTCGAATGGCAAAGCACATTAAAGACATTTCCACAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - ggtttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtttga