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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattttgctgccataatagattgacttctcgcttctcttatatcacttagtaatatggcctttagtcaagttgttaatatatatatggttattgtgaatacagAATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACCAAGGACCGAAGGCTCCAAGCGCAGCAACTTGACAAATTGCTCTATGTAG

Basic information

species Zea mays
transcript GRMZM2G136178_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136178_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g35130.2 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------------------------------gttattttgctgccataatagattgacttctcgcttctcttatatcacttagtaatatggcctttagtcaagttgttaatatatatatggttattgtgaatacagAATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACCAAGGACCGAAGGCTCCAAGCGCAGCAACTTGACAAATTGCTCTATGTAG
                                                                                 || ||  ||    |  ||| | ||  ||            || |  || |  |  ||||    ||  |    ||| | || |||||||  | || |   |||||||   ||||||||||||| |||||||||||||  |||| ||||| | ||||||||||||| ||||||||| | |||||||||| || |||||  |||| |
gtaacattttttttttgttgaaacttctatgcacatgctaaataataatatcccgatggaatctgcaggcgggatttcaattttttccgcgtagaatataaagtgcatttgatgaaagaaaattttcctcatgagcatggttcatatactttatgtaattacatatatg--tgttttatttacagAAAACTGTTGAGCTATGCAAAAACAGAGTTGTTCTCTTTGATAATATGACCAAGGACCGATGGCTCCAAGAGAAGCAACTTGAAAATTTGCTTGATGTTG
















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|211073416|gb|FL140891.1|FL140891
EST:     TGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAG                         AATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACC
genomic: TGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAGgttattttgc ... gtgaatacagAATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACC
EST: gi|60396244|gb|DN229113.1|DN229113
EST:     GTGAATCTAAGTTGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAG                         AATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACC
genomic: GTGAATCTAAGTTGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAGgttattttgc ... gtgaatacagAATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACC
EST: gi|67030328|gb|CO459077.1|CO459077
EST:     GTGAATCTAAGTTGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAG                         AATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACC
genomic: GTGAATCTAAGTTGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAGgttattttgc ... gtgaatacagAATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACC
EST: gi|116824035|gb|EC867618.1|EC867618
EST:     GTGAATCTAAG-TGAAGAACATGCTCAATGATGCG-CA-AGTATTTGCAG                         AATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACC
genomic: GTGAATCTAAGTTGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAGgttattttgc ... gtgaatacagAATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACC
EST: gi|74052546|gb|DN591141.1|DN591141
EST:     GTGAATCTAAGTTGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAG                         AATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACC
genomic: GTGAATCTAAGTTGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAGgttattttgc ... gtgaatacagAATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

AAAGATTGTTGACCACATGGTTTTAGTTTTTACTTATGGTGATCTAGTTGGTGAATCTAAGTTGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAGgttattttgc ... gtgaatacagAATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACCAAGGACCGAAGGCTCCAAGCGCAGCAACTTGACAAATTGCTCTATGTAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 161

AAAGATTGTTGACCACATGGTTTTAGTTTTTACTTATGGTGATCTAGTTGGTGAATCTAAGTTGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAGgttattttgc ... gtgaatacagAATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACCAAGGACCGAAGGCTCCAAGCGCAGCAACTTGACAAATTGCTCTATGTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

AAAGATTGTTGACCACATGGTTTTAGTTTTTACTTATGGTGATCTAGTTGGTGAATCTAAGTTGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAGgttattttgc ... gtgaatacagAATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACCAAGGACCGAAGGCTCCAAGCGCAGCAACTTGACAAATTGCTCTATGTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 163

AAAGATTGTTGACCACATGGTTTTAGTTTTTACTTATGGTGATCTAGTTGGTGAATCTAAGTTGAAGAACATGCTCAATGATGCGCCAGAGTATTTGCAGgttattttgc ... gtgaatacagAATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACCAAGGACCGAAGGCTCCAAGCGCAGCAACTTGACAAATTGCTCTATGTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaatatggcctttagtcaagttgttaatatatatatggttattgtgaatacagAATGTTGTTGAGCTATGCCAAAACAGAGTTGTCGTCTTCGATAACAGGACCAAGGACCGAAGGCTCCAAGCGCAGCAACTTGACAAATTGCTCTATGTAG
                       tgttaat  putative branch site (score: 163)
                         ttaatatatatatggt  TA-rich tract