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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattccttgatctttcaagcatattttctttctaggattggctatatcatcaactgatcctctttctcacagcgatttttgttttcagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTGGTTCATTTGCAG

Basic information

species Zea mays
transcript GRMZM2G047695_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047695_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g13460.1 (Oryza sativa), 3'ss of exon 4
---gtattccttgatctttcaagcatattttctttctaggattggctatatcatcaactgatcctctttctcacagcgatttttgttttcagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTGGTTCATTTGCAG
    | |   |||| ||| |||     |  | | ||| |||||  || |  ||  | ||| |  |  ||||||   | | | || |   |||||||||||||||||||||||||| ||||||||||| ||||| || |||||||| |||||||| |||||||||||||| ||||| |||||||||
gtgctttcttttgaccttccaaaatgttcctgtctctgggatt--ctgttgcactagctgcttgttgttctcatgtcaactgttatg--cagCAATATCCTTTTGACATACCTACCGAGGCTTTTCCATTTGAGATCTTCAAGCAAGCTTTTGTCGCAGTACAGTCTTGCGTGGTCCATTTGCAG

upper sequence: GRMZM2G047695_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G22520.2 (Glycine max), 3'ss of exon 4
gtattccttgatctttcaagcatattttctttctaggattggctatatcatcaactgatcctctttctcacagcgatttttgttttcagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTGGTTCATTTGCAG
||| |      |    | | ||  ||   |   || | |    | |   ||  | || |    ||  |  ||   || |     | ||||||||||| | |||||| ||||||||||| ||| | ||||| || ||||| || || |||| |||  | |||||||||||||| ||||| |||
gtaataaa-atttccccgaacaagttcagtagttatg-tacattttgagatttagtgcttacattatttgcataaatat---aatgcagCAATATCCATATGACATTCCTACTGAGGCCTTTTCATTTGAGATTTTCAAACAAGCCTTTGCTGCTATTCAGTCTTGTGTGGTGCATTTACAG

upper sequence: GRMZM2G047695_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G14260.2 (Arabidopsis thaliana), 3'ss of exon 4
-------gtattccttgatctttcaagcatattttctttctaggattggctatatcatcaactgatcctctttctcacagcg----atttttgtttt-cagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTGGTTCATTTGCAG
       |    |   ||| |      | | || || || ||  ||  |  ||   |   |  |  ||||   || ||| |     |||| |||||| |||||||| || ||||||||||| ||||| |||||| | ||||| || ||||| ||||| ||||||||  | ||||| |||||||| ||||| || 
gtgtttggctacctacgatttcggcttcttcttgtcattttaatatatggaatgctaaacatcgg-cctcggacttacaccattttatttgtgttttgcagCAATACCCATTTGACATACCAACTGAAGCTTTTTCATTTGAGATTTTCAAACAGGCATTTGTTGCCATTCAGTCATGTGTGGTGCATTTACAA

upper sequence: GRMZM2G047695_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0171g00310.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------------------------------gtattccttgatctttcaagcatattttctttctagg--attggctatatc---atcaac-tgatcctctttctcacagcgatttttgttttcagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTGGTTCATTTGCAG
                                                                                 ||||    |||  ||  |  | ||| |  || ||||  ||| | || ||    || ||  |||   |  || ||  |   |||| | ||| |||||||| || | ||| || ||||||||||| ||||| ||||| || ||||| || |||||||||||| | |||||||||||||| ||||| |||
gtcattctcttacacatctgttgttgaaactagataatatatgccttccccttttgttaatttaaatatattgctgtttcctattgggagattctttgattacattgttcttttaggtgatttgttaaatgtagatgaatgtgactatgattttctta---atttctttttgcagCAATACCCATATGATATTCCTACTGAGGCCTTTCCATTTGAGATTTTCAAACAAGCTTTTGTTGCAATTCAGTCTTGTGTGGTGCATTTACAG

upper sequence: GRMZM2G047695_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S181_117V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------gtattccttgatctttcaagcatattttctttctaggattggctatatca-tcaactgatcctctttctcacagcgattt-----ttgtttt--cagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTGGTTCATTTGCAG
                                           ||||   |  |||||      |||||| |     ||||||      |  | |   |||||  |  |||  |||  | ||      || |||   ||||||||||| || ||| ||||||| || |||||  | ||||| |||||||||||||||||||| || || ||||| || || |||||  | |||
gtaattccactgccgactttacattatgagatgaagctgaagagtatgt-tccatcttggtgagatatttgca---gaggattacggggagaagtttgctgatgattcttcaaacattggttgcctggttatttaaacagCAATATCCCTTCGACCTACCTACGGAAGCTTTCTCATTTGAGATATTCAAGCAGGCTTTTGTGGCTGTGCAGTCCTGCGTTGTTCACCTCCAG

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|31350131|gb|CD434488.1|CD434488
EST:     AGTATAATGAGCTTGACACATTGTGGTTTATGGCAGGTTCACTATTTCAG                         CAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAG
genomic: AGTATAATGAGCTTGACACATTGTGGTTTATGGCAGGTTCACTATTTCAGgtattccttg ... ttgttttcagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAG
EST: gi|71437981|gb|DR819031.1|DR819031
EST:     AGTATAATGAGCTTGACACATTGTGGTTTATGGCAGGTTCACTATTTCAG                         CAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAG
genomic: AGTATAATGAGCTTGACACATTGTGGTTTATGGCAGGTTCACTATTTCAGgtattccttg ... ttgttttcagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggattggctatatcatcaactgatcctctttctcacagcgatttttgttttcagCAATATCCTTTTGACATACCTACTGAGGCTTTTCCGTTTGAAATATTCAAGCAGGCTTTTGTTGCAGTACAGTCTTGTGTGGTTCATTTGCAG
                              ttctcac  putative branch site (score: 2)
                                          tttttgttttc  putative PPT
                                         atttttgtttt  TA-rich tract