Sequence
atgc intronic sequence ATGC exonic sequencegtaagttaatgcagttttcagaatttttttacacttcttcaatctcctagatttagattttagatctaactgagcaggattccattactaaattattatttttatatatgaaccacaaacttcttcagGCTCAATCTGCATCCATGGCAGAGATATGGCTATGGGAGGTTGGGACATGGAAAGCTGTTGGTCGTTTGCAATCTCACAGCTTGACGGTGACGCACTTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G49540.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G49540.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os08g38570.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------gtaagttaatgcagttttcagaatttttttacacttcttcaatctcctagattta---------gattttagatctaactgagcaggattccattactaaattattatttttatatatgaaccacaaacttcttcagGCTCAATCTGCATCCATGGCAGAGATATGGCTATGGGAGGTTGGGACATGGAAAGCTGTTGGTCGTTTGCAATCTCACAGCTTGACGGTGACGCACTTGG
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gtaatgtatatctctggagtctggatatccatgaaatattttatcacatcttgtctggaaataacacatttctcaatttgtcctcatgtatggcatagtaacattagttcatgcactttatgctcgtagtttggcttgacgagtgtgatgtagtaatgtgaccttgttgcagGCTCAATCAGCACCAGTTGCTGAGATCTGGCTGTGGGAGGTTGGAACATGGAAAGCTGTTGGCCGCCTGCAATCTCACAACCTGACAGTTACACAGATGG
upper sequence: AT1G49540.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G042371_T01 (Zea mays), 3'ss of exon 5
gtaagttaatgcagttttcagaatttttttacacttcttcaatctcctagatttagattttagatctaactgagcaggattccat--tactaaat-tattatttttatatatgaaccacaaacttcttcagGCTCAATCTGCATCCATGGCAGAGATATGGCTATGGGAGGTTGGGACATGGAAAGCTGTTGGTCGTTTGCAATCTCACAGCTTGACGGTGACGCACTTGG
|| ||| | || || | | ||| | ||| | | | || || |||| || || ||| ||| || | ||||||||||||| ||| | | |||||||| ||||| ||||||||||| |||||||||||||||| || |||||||||||||| | || ||||| || |||
---------------------------ttgacataattaca-tcagttgatgctggatat---gcttaattattaatggtttgattttactgtatgcatgggaaatatgatggaatttcactcccattcagGCTCAATCAGCAGCAGTTGCAGAGATCTGGCTCTGGGAGGTTGGAACATGGAAAGCTGTTGCCCGCTTGCAATCTCACAGTCTAACAGTGACACAAATGG
upper sequence: AT1G49540.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv01s0011g04130.t01 (Vitis vinifera), 3'ss of exon 8
gtaagttaatgcagttttcagaatttttttacacttcttcaatctcctagatttagattttagatctaactgagcaggattccattactaaattattatttttatatatgaaccacaaacttcttcagGCTCAATCTGCATCCATGGCAGAGATATGGCTATGGGAGGTTGGGACATGGAAAGCTGTTGGTCGTTTGCAATCTCACAGCTTGACGGTGACGCACTTGG
| || || || | |||| || || || || | || | ||| || ||| || || || | |||||||| | || | || | || | ||||||||||| || | ||||| |||||||||||| | || || ||||||| || |||||||| ||||||||||||||||| || ||||| || | |
--gatgtatagctgtatgtagaac----ttgcatttttttaccctgt--gtttttga---taggcata---------gaagttgttgc-aaattattgct------catagattgcata-ttttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGGAAGGCAGTTGGTCGCTTGCAATCTCACAGCTTAACAGTGACACAGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaggattccattactaaattattatttttatatatgaaccacaaacttcttcagGCTCAATCTGCATCCATGGCAGAGATATGGCTATGGGAGGTTGGGACATGGAAAGCTGTTGGTCGTTTGCAATCTCACAGCTTGACGGTGACGCACTTGG
tactaaa putative branch site (score: 1)
cttcttc putative PPT
attactaaattattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttaatgcagttttcagaatttttttacacttcttcaatctcctagatttagattttagatctaactgagcaggattccattactaaattattatttttatatatgaaccacaaacttcttcagGCTCAATCTGCATCCATGGCAGAGATATGGCTATGGGAGGTTGGGACATGGAAAGCTGTTGGTCGTTTGCAATCTCACAGCTTGACGGTGACGCACTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT