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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctccctttgatttccggctggattggggtggattgttgcgcgttgctttgattgggcctcgtcgtggctccatatctaatggtcgattttggtttggctggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAGTGGC

Basic information

species Zea mays
transcript GRMZM2G177276_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G177276_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g09330.1 (Oryza sativa), 3'ss of exon 1
gtgagctccctttgatttccggctggattggggtggattgttgcgcgttgctttgattgggcctcgtcgtggctcc-atatctaatggtcgattttggtttggctggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAGTGGC
|||||        | | ||||  ||||||||  | |||||    | |||| |  ||||||   |||  | |  ||  ||   |     ||| |||||| | ||  ||||| ||||||||||| |||||||||||||||||||||||||||||||||||| |||||||||
gtgag--------gctctccgtgtggattggatttgattggattgtgttgatgcgattgg-tttcgatgcgattctgatggttttgtttcggttttgggt-ggtcggattgcagGAGCCGCCGCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATATTGGAGTGGC
















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|211352550|gb|FL243583.1|FL243583
EST:     AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|211489813|gb|FL245176.1|FL245176
EST:     AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTTGCTCGCCCGCTGCCCAACGACATACTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|32945073|gb|CF049892.1|CF049892
EST:     GAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTTTTCTATG                         GAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGA
genomic: GAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGC-AAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGA
EST: gi|211352548|gb|FL243581.1|FL243581
EST:     AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|37396958|gb|CF635773.1|CF635773
EST:     CCAGAAGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTTGCTCGCCCGCTGCCCAACGACATACTGGAG
genomic: CCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|32798352|gb|CD950588.1|CD950588
EST:     AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTGGCTTGCCCGCTGCCCAACGACATACTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|211486943|gb|FL245173.1|FL245173
EST:     AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTTGCTCGCCCGCTGCCCAACGACATACTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|31355568|gb|CD439925.1|CD439925
EST:     AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGTCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|211486944|gb|FL245174.1|FL245174
EST:     ANAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCCAACGACAT
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCC-AACGACAT
EST: gi|211486945|gb|FL245175.1|FL245175
EST:     AVAAGGGCTGCCTCAAGCGGCTCCAGAAGGAKTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATASTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|211352549|gb|FL243582.1|FL243582
EST:     AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|32795477|gb|CD947713.1|CD947713
EST:     AGAAGGGCTGCCTCAAGCGGCTCCAGAGGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCGGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|211489815|gb|FL245178.1|FL245178
EST:     AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCC-AACGACATACTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|76925875|gb|DV170632.1|DV170632
EST:     AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|78120787|gb|DV539171.1|DV539171
EST:     AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
EST: gi|211389693|gb|FL031644.1|FL031644
EST:     AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAG                         GAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG
genomic: AGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAG

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: 168

GTTTCGGCGGGTGCGGTCGCCGTGTAGGCGGTAGGGTTTTGCCATGGCGGAGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAGTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

GTTTCGGCGGGTGCGGTCGCCGTGTAGGCGGTAGGGTTTTGCCATGGCGGAGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAGTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

GTTTCGGCGGGTGCGGTCGCCGTGTAGGCGGTAGGGTTTTGCCATGGCGGAGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAGTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

GTTTCGGCGGGTGCGGTCGCCGTGTAGGCGGTAGGGTTTTGCCATGGCGGAGAAGGGCTGCCTCAAGCGGCTCCAGAAGGAGTACCACGCCCTCTGCAAGgtgagctccc ... tggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAGTGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggcctcgtcgtggctccatatctaatggtcgattttggtttggctggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAGTGGC
                    atctaat  putative branch site (score: 114)
                  atatctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctccctttgatttccggctggattggggtggattgttgcgcgttgctttgattgggcctcgtcgtggctccatatctaatggtcgattttggtttggctggattacagGAGCCGCCTCCGCAGATCGTGGCTCGCCCGCTGCCCAACGACATACTGGAGTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT