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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctcatctcccccgaatgtttcatcaattattgctttctggtgggtgctcagtgctcactttgtatttggtttggtttttgtttgaaaaaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATCATAGTGACCAGCATTGATGGGAGAAATGGGCAGGCAAAGCAG

Basic information

species Zea mays
transcript GRMZM2G155836_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g04340.2 (Oryza sativa), 3'ss of exon 2
gtaatctcatctcccccgaatgtttcatcaattattgctttctggtgggtgctcagtgctcactttgtatttggtttggtttttgtttgaaaaaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATCATAGTGACCAGCATTGATGGGAGAAATGGGCAGGCAAAGCAG
                    | ||    | |  | || |   |  | | |||       |  || | |  |  |||     |||| || | |||    ||||||| |||| || || || ||||||||||||||| | || ||||||||| | || ||||| ||||||||||| |||||||| ||||| || |||
-------------------gtattatgcctaagagtggtggatcatagttgcct----tttgctgtattgtcagttgctgatttgattcacaaacgtcgcagGACATTGACGACATAGTTGTCAATGGCAATGGGACAGAACCTGGTCATGTTATTGTGACAAGCATTGATGGAAGAAATGGACAGGCTAAACAG
















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|149089860|gb|EE179141.2|EE179141
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|71315008|gb|DR794124.1|DR794124
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|87154289|gb|DY399078.1|DY399078
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|149111565|gb|EE190699.2|EE190699
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|89253101|gb|DY624887.1|DY624887
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|211396327|gb|FL436147.1|FL436147
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|76927490|gb|DV171263.1|DV171263
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|211206254|gb|FL246828.1|FL246828
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGA-C-TGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|21390766|gb|BQ528815.1|BQ528815
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|19058579|gb|BM737246.1|BM737246
EST:     GTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGATAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: GTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|148971909|gb|EE022686.2|EE022686
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|148932063|gb|EC875411.2|EC875411
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|149009140|gb|EE041278.2|EE041278
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|149078458|gb|EE167238.2|EE167238
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|148961324|gb|EE012052.2|EE012052
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|60401199|gb|DN234006.1|DN234006
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|5566821|gb|AI881687.1|AI881687
EST:     GTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: GTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|74234442|gb|DT642356.1|DT642356
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGTGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|149095924|gb|EE181586.2|EE181586
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
EST: gi|71446043|gb|DR827093.1|DR827093
EST:     CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAG                         GACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC
genomic: CAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATC

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: 48 (upstream exon), 49 (downstream exon)
Score: 117

GGCACGCTCTTCTTTGGGATTTCAGAATGGCACAAGTTCTAGCAGTGACCCAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATCATAGTGACCAGCATTGATGGGAGAAATGGGCAGGCAAAGCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 131

GGCACGCTCTTCTTTGGGATTTCAGAATGGCACAAGTTCTAGCAGTGACCCAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATCATAGTGACCAGCATTGATGGGAGAAATGGGCAGGCAAAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

GGCACGCTCTTCTTTGGGATTTCAGAATGGCACAAGTTCTAGCAGTGACCCAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATCATAGTGACCAGCATTGATGGGAGAAATGGGCAGGCAAAGCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 122

GGCACGCTCTTCTTTGGGATTTCAGAATGGCACAAGTTCTAGCAGTGACCCAGATCGTCTTCCCAACGAGTTGGGCAGTATGAGCATAAGGGACGACAAGgtaatctcat ... aaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATCATAGTGACCAGCATTGATGGGAGAAATGGGCAGGCAAAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtgctcagtgctcactttgtatttggtttggtttttgtttgaaaaaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATCATAGTGACCAGCATTGATGGGAGAAATGGGCAGGCAAAGCAG
         tgctcac  putative branch site (score: 122)
                                tttttgtttgaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctcatctcccccgaatgtttcatcaattattgctttctggtgggtgctcagtgctcactttgtatttggtttggtttttgtttgaaaaaaaatgcagGACGTTGAAGATATTGTAGTCAATGGCAATGGGGCGGAGCCTGGTCATATCATAGTGACCAGCATTGATGGGAGAAATGGGCAGGCAAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG