Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G50950.2 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacc--tcaatgctaattcctcctttac-----cagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG
|||||| | ||| | | ||||| || | | ||| || || || |||||| || || | || || | | || || | ||||||||||||||||||||||||||||| || || || | ||| |||||||||||| ||||||| |||
gtaagt-----gaaattcatccattttgt--agccttacat-ttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG
upper sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 15
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG
|||||| |||| || | | || | | ||| | || | || | | | | ||| || | || || | || | |||||||||||||||||||||||||||| || || || | ||| |||||||||||| ||| || |||
gtaagta---aaatgaaaatttaccttttttaaatatctgt-ttgtggttgtaaaaagtagtgagccatgctta---ctttttgaacgattgc-agAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG
upper sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA10G02040.2 (Glycine max), 3'ss of exon 15
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG----------------------------------
|||||| || | | || |||| || | || ||| |||| | | | || |||||||| ||| || || |||||||||||| |||||||| || |||||||| ||||| | ||| |||||||| || || || | |||
gtaagtgtcctcttgt----ctacttttgtaacttgctaattttcacatttttttaaaaactgaattta-----------atttgtctgtt-ccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAGGTGATGATGCCATGTTATACTTGTTTTTCCGTTT
upper sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA10G02040.1 (Glycine max), 3'ss of exon 15
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG
|||||| || | | || |||| || | || ||| |||| | | | || |||||||| ||| || || |||||||||||| |||||||| || |||||||| ||||| | ||| |||||||| || || || | |||
gtaagtgtcctcttgt----ctacttttgtaacttgctaattttcacatttttttaaaaactgaattta-----------atttgtctgtt-ccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
upper sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 15
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG
|||||| || | | ||||| | || | || ||| ||| | || ||| | | || | | ||| | ||||||||||| |||||||| || |||||||| ||||| | ||| |||||||| || || || | |||
gtaagtgtcctcttgt----cttctccggtaacttgctaattttcacatatt--ttttaaacggaattg-----------aatttgcctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
upper sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv14s0060g01700.t01 (Vitis vinifera), 3'ss of exon 13
-----------------------------gtaagtctctaaatattaa----acttctttgtcaagtcatccatatt---ctcattatgat-----tacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG
||| ||| || ||| | | || || | || | ||| | | || || || | | |||| |||| || | | | | || | |||||||||| |||||||| ||||||||||| || ||||| | ||||||||| || ||| ||| | |||
gtgagtgtttttcctccgccatcatttgtttaatcatcttaagattcagtccattttatttttaaattttccttctctgcctacttgtgttggatgtggcaatggattttgatcgac-tttttacttcatgaaccagAAAATCGGCTATGATAATGCTGCAGCGGTTGCCAAGAAAGCTCACAAGGAGGGAACCACTCTTAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86080103|gb|DR375860.1|DR375860EST: TCTCTTATGCTTGTGACATCATTGAATCCT AAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAA
genomic: TCTCTTATGCTTGTGACATCATTGAATCCTgtaagtctct ... cctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAA
EST:
gi|116428257|gb|EG470849.1|EG470849EST: TCTCTTATGCTTGTGACATCATTGAATCCT AAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAA
genomic: TCTCTTATGCTTGTGACATCATTGAATCCTgtaagtctct ... cctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAA
EST:
gi|86075192|gb|DR370949.1|DR370949EST: TCTCTTATGCTTGTGACATCATTGAATCCT AAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAA
genomic: TCTCTTATGCTTGTGACATCATTGAATCCTgtaagtctct ... cctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG