Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAAACAATAAACTATTAACGTTTTCATCACTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50950.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50950.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacc--tcaatgctaattcctcctttac-----cagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAAACAATAAACTATTAACGTTTTCATCACTAA
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gtaagt-----gaaattcatccattttgt--agccttacat-ttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG----------------------------------
upper sequence: AT5G50950.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 15
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAAACAATAAACTATTAACGTTTTCATCACTAA
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gtaagta---aaatgaaaatttaccttttttaaatatctgt-ttgtggttgtaaaaagtagtgagccatgctta---ctttttgaacgattgc-agAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG----------------------------------
upper sequence: AT5G50950.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 15
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAA--ACAATAAACTATTAACGTTTTCATCACTAA
|||||| || | | || |||| || | || ||| |||| | | | || |||||||| ||| || || |||||||||||| |||||||| || |||||||| ||||| | ||| |||||||| || || || | ||||| | | | ||| ||||| |
gtaagtgtcctcttgt----ctacttttgtaacttgctaattttcacatttttttaaaaactgaattta-----------atttgtctgtt-ccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAGGTGATGATGCCATGTTATACTTGTTTTTCCGTTT--
upper sequence: AT5G50950.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA10G02040.1 (Glycine max), 3'ss of exon 15
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAAACAATAAACTATTAACGTTTTCATCACTAA
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gtaagtgtcctcttgt----ctacttttgtaacttgctaattttcacatttttttaaaaactgaattta-----------atttgtctgtt-ccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG----------------------------------
upper sequence: AT5G50950.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 15
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAAACAATAAACTATTAACGTTTTCATCACTAA
|||||| || | | ||||| | || | || ||| ||| | || ||| | | || | | ||| | ||||||||||| |||||||| || |||||||| ||||| | ||| |||||||| || || || | |||
gtaagtgtcctcttgt----cttctccggtaacttgctaattttcacatatt--ttttaaacggaattg-----------aatttgcctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG----------------------------------
upper sequence: AT5G50950.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv14s0060g01700.t01 (Vitis vinifera), 3'ss of exon 13
-----------------------------gtaagtctctaaatattaa----acttctttgtcaagtcatccatatt---ctcattatgat-----tacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAAACAATAAACTATTAACGTTTTCATCACTAA
||| ||| || ||| | | || || | || | ||| | | || || || | | |||| |||| || | | | | || | |||||||||| |||||||| ||||||||||| || ||||| | ||||||||| || ||| ||| | |||
gtgagtgtttttcctccgccatcatttgtttaatcatcttaagattcagtccattttatttttaaattttccttctctgcctacttgtgttggatgtggcaatggattttgatcgactttt-tacttcatgaaccagAAAATCGGCTATGATAATGCTGCAGCGGTTGCCAAGAAAGCTCACAAGGAGGGAACCACTCTTAAG---------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAAACAATAAACTATTAACGTTTTCATCACTAA
tgctaat putative branch site (score: 2)
ttcctcctttacc CT-rich tract
attatgattacaaatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAAACAATAAACTATTAACGTTTTCATCACTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG