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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattttatattgactggctatttagatttttttatcttataacacttcttagttctacagattatctgttttaggttatttttgtcttacaacatgtcttcacagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAGAATGGTGAAGTT

Basic information

species Zea mays
transcript GRMZM2G108829_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 1
gtaaattttatattgactggctatttagatttttttatcttataacacttcttagttctacagattatctgttttaggttatttttgtcttacaacat-----gtcttcacagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAGAATGGTGAAGTT
                                              |  | | |  |  ||  | |||   |||||||| |  ||| |||||  |  |     |||||  |||||||||  |||||||||||||||| || |||||||||||||||||||||||||||||||||||||| ||||||||||||
--------------------------------------------gtaactttcatattgacttactat---ttttaggtcacctttttcttatcaagtatgttgtctttgcagATTCAAAATGATTAAGGAAGTTGGTGACGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAAAATGGTGAAGTT

upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G35190.2 (Glycine max), 3'ss of exon 1
gtaaattttatattgactggctatttagatttttttatcttataacacttcttagttctacagattatctgttttaggttatttttgtctta-caacatgtcttcacagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAGAATGGTGAAGTT
                   |  ||||    ||| |  | ||  |  | ||  || |  | |   || | | || |  ||| ||||| |   |   || ||     |||| | |||||| |||||||||||||| ||||||||||| |||||||| ||| | ||||| ||||| || |  |||||||||
-------------------gtgattt---ctttctctttttgcagaagttacta-tagtcccccttgtttattgttagttttttttattaaaattacctgcaaatacagGTACAAGTTAATTAAGGAAGTTGGTGATGGGACTTTTGGGAGTGTCTGGAGAGCTATTAATAAGCAAACCGGTGAAGTT

upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G19110.1 (Arabidopsis thaliana), 3'ss of exon 3
----gtaaattttatattgactggctatttagatttttttatcttataacacttcttagttctacagattatctgttttaggttatttttgtcttacaacatgtcttcacagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAGAATGGTGAAGTT
     | | |||| | |  ||| | | ||||   | ||||   | ||    |  |||  || |   | ||||  ||||   ||| |   || ||||  | || |||    || | |||||| ||||| || ||||| ||||| ||||| || ||||| ||||| ||||||||||| ||||  |||||||| 
gtagcttagttttctctcaacttgttttttaatatctttt---tcatcgggccccttgatt-tgtggcttatgagttt--agttctcaatgccttatga-atttct----agGTACAAGTTAATTAAAGAGGTTGGTGATGGAACTTTTGGTAGTGTTTGGCGAGCTATAAATAAGCAGACGGGTGAAGTC

upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 1
gtaaattttatattgactggctatttagatttttttatcttataacacttcttagttctacagattatctgttttaggttatt--tttgtcttacaacat--gtcttcacagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAGAATGGTGAAGTT
                         |   |    ||    |||   ||||  | |||    |   | | | |||||   | ||  | ||||| | |   |  | ||  |||| |  | | | || ||||||||||| ||||||||||| || ||||| ||||| || |||||||| |||| ||||||||||
------------------------gtgagtgggcttg---tatggaacttgcttgtt----aatatttgtattttaatgtgttgatatgtctgagagttttggcctctacagGTATACGATAATCAAGGAAGTTGGTGATGGGACTTTTGGAAGTGTTTGGCGAGCAATAAATAAGCAGACTGGTGAAGTT

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|47961778|gb|CN844487.1|CN844487
EST:     TGAAGGGGAAAATTTGCACGAGACACCTCGGATATTACAACAATGGATAG                         ATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTCGGNAGTGTATGGCG
genomic: TGAAGGGGGAAATTTGCACGAGACACCTCGGATATTACAACAATGGATAGgtaaatttta ... gtcttcacagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTCGGGAGTGTATGGCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttctacagattatctgttttaggttatttttgtcttacaacatgtcttcacagATTCAAGTTGATTAAGGAAGTTGGCGATGGGACTTTCGGGAGTGTATGGCGTGCTATAAATAAACAGAATGGTGAAGTT
                                 gtcttac  putative branch site (score: 3)
                                            tgtcttc  putative PPT
                  ttttaggttattttt  TA-rich tract