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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtattactttgcttgatgtatgggatgtcttcatctcaatcttctttaagaaattcttttctgcattatgtctgggttttaataagtagcatattactcgcagATATCTCCTCGACAAGGGCTTCTTAGAGTTCGTGAATTCACGCTGGCAGAGATTGAGCACTTCGTTGATCCTGAGAATAAGTCACATCCTAAGTTCTCTG

Basic information

species Arabidopsis thaliana
transcript AT1G29880.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g42560.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------------------gtaatgtattactttgcttga---tgtatgggatgtcttc----atctcaatcttctttaagaaattctt--ttctgcattatgtctgggttttaataagtagcatattactcgcagATATCTCCTCGACAAGGGCTTCTTAGAGTTCGTGAATTCACGCTGGCAGAGATTGAGCACTTCGTTGATCCTGAGAATAAGTCACATCCTAAGTTCTCTG
                                                                         | | ||   || |   | |   ||  | |||     ||    ||  ||   || ||||     |||||  || ||  ||||  ||   | ||  ||  || |||   | ||  |||| ||||| |||||||| |||||  | || |||||||||||  | || |||||||||||||| || ||||||||| |||| || || || || ||   ||
gtctgtgttttgatacattttgtctttgcgttctgcatttcgattatatgcttgaaggagtctagacttattgactataggtctatagctaactatgcttaggaaactctccactatgccatggttttttagagggttctttcttttgtgttata-ctcactgtttcta--taccatgcaaatc--agATTTCTCCACGACAAGGTCTTCTACGTGTGCGTGAATTCACATTAGCCGAGATTGAGCACTTTGTGGATCCTGAGGATAAATCTCACCCAAAATTTGTTG

upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G041797_T01 (Zea mays), 3'ss of exon 3
gtaatgtattactttgcttgatgtatgggatgtcttcatctcaatcttctttaagaaattcttttctgcattatgtctgggttttaataagtagcatattactcgcagATATCTCCTCGACAAGGGCTTCTTAGAGTTCGTGAATTCACGCTGGCAGAGATTGAGCACTTCGTTGATCCTGAGAATAAGTCACATCCTAAGTTCTCTG
     | | |||||||||| |   |   | | |   |    ||||  |   | ||| |||| ||| |  |   |            |    | | |  | ||   ||||| || || |||||||| |||||  |||| |||||||||||  |||||||||||||||| || || || || ||| | || |||||||| || ||   ||
---tagcaatactttgcttcaaaaagcagttattggctaagcaatagttgcttagatattcctttttttaacgtactca-----ctacgtctggaacttgacaatcagATCTCGCCACGACAAGGTCTTCTCCGAGTGCGTGAATTCACATTGGCAGAGATTGAGCATTTTGTGGACCCAGAGGACAAATCACATCCAAAATTTGTTG

upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM5G821551_T02 (Zea mays), 3'ss of exon 3
gtaatgtattactttgcttgatgtatgggatgtcttcatctcaatcttctttaagaaattcttttctgcattatgtctgggttttaataagtagcatattactcgcagATATCTCCTCGACAAGGGCTTCTTAGAGTTCGTGAATTCACGCTGGCAGAGATTGAGCACTTCGTTGATCCTGAGAATAAGTCACATCCTAAGTTCTCTG
   ||   |  | |   |  |   |   | | |   |   |||||  |   | ||| |||| ||| |   | | ||      |   ||   ||| |  | ||   ||||| || || |||||||| |||||  |||| |||||||||||  |||||||||||||||| || || || || ||| | || |||||||| || ||   ||
---atagttagcatgcttctaaaaagcagttattggctattcaatagttgcttagatattcctttttt--tcaagtactcact---atgtctagaacttgacaatcagATCTCGCCACGACAAGGACTTCTCCGAGTCCGTGAATTCACATTGGCAGAGATTGAGCATTTTGTGGACCCAGAGGACAAATCACATCCAAAATTTGTTG

upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G47890.1 (Glycine max), 3'ss of exon 1
gtaa-tgtattactttgcttgatgtatgggatgtcttcatctcaatcttctttaagaaattcttttctgcattatgtctgggttttaataagtagcatattactcgcagATATCTCCTCGACAAGGGCTTCTTAGAGTTCGTGAATTCACGCTGGCAGAGATTGAGCACTTCGTTGATCCTGAGAATAAGTCACATCCTAAGTTCTCTG
||   |  || | |||  | |   | | |  | | ||  | | |  |||  | ||  |  | |  |||     |||  | || ||  ||  || |  | |   |   |||||||||| ||||| |||||||| ||||| || || |||||| |||| |||||||||||||| ||||| |||    ||||||| ||||| |||| | |||
gtgggttcatgattttcgtggcaatttagactttattttttttatactttctaaattagatatagtctttgc-atgaattgggttggat--gttgtttgtgtgtt-tagATATCTCCACGACAGGGGCTTCTGAGAGTGCGGGAGTTCACGTTGGCGGAGATTGAGCACTTTGTTGACCCTCTAGATAAGTCTCATCCCAAGTACCCTG

upper sequence: AT1G29880.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0150g00150.t01 (Vitis vinifera), 3'ss of exon 3
gtaatgtattactttg--cttgatgtatgggatgtcttcatctcaatcttctttaagaaattcttttctgcattatgtctgggttttaataagtagcatattactcgcagATATCTCCTCGACAAGGGCTTCTTAGAGTTCGTGAATTCACGCTGGCAGAGATTGAGCACTTCGTTGATCCTGAGAATAAGTCACATCCTAAGTTCTCTG
 |  ||  |   ||||  |||| | ||       | |  |   | |||| |||     || |        |||||  ||||     |||| | |  | ||    ||  |||||||||| || ||||| ||| | |||||||| || |||||  |||||||||||||| |||| |||||||||||  | || || || || || |  ||||
-ttttggttctttttggtcttggtttacttataatttggagggctatctccttagccgaaatgc---acacattaaatctga----taatgatttccttaaagttc--agATATCTCCCCGCCAAGGCCTTTTGAGAGTTCGCGAGTTCACATTGGCAGAGATTGAGTACTTTGTTGATCCTGAAGACAAATCTCACCCCAAATATTCTG

Mapped 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|116404822|gb|EG447414.1|EG447414
EST:     AGAAACTTCCTTTTGCCGCGGCTCAAAT-GGTCAAGCCTTTAGAAATGAG                         ATATCTCCTCGA
genomic: AGAAACTTCCTTTTGCCGCGGCTCAAATTGGTCAAGCCTTTAGAAATGAGgtaatgtatt ... ttactcgcagATATCTCCTCGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaattcttttctgcattatgtctgggttttaataagtagcatattactcgcagATATCTCCTCGACAAGGGCTTCTTAGAGTTCGTGAATTCACGCTGGCAGAGATTGAGCACTTCGTTGATCCTGAGAATAAGTCACATCCTAAGTTCTCTG
                            ttttaat  putative branch site (score: 3)
                            ttttaataagta  TA-rich tract