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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggctaagactggcattgtttggcataccacaatatattagatgtcttaactcttcgaatttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGATGGTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCC

Basic information

species Zea mays
transcript GRMZM2G060977_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060977_T05 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 11
gtgcggctaagactgg--cattgtttggcataccacaatatattagatgtcttaac-tcttcgaatttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGATGGTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCC
||  || |||||||    |||||||||  |  |   | ||| |||    ||| ||| | ||| ||||    |  ||||||| |||||||| || || ||||||||||| ||||||||||| |||||||| ||||||||||| || |||||||| ||||| |||||||||||||| |
gtaaggttaagactttctcattgtttgtaa--ctgtactatgttaa---tctcaaccttttctaattgtattgaagGACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGATGAGGGTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGAC
















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|211495481|gb|FL464081.1|FL464081
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|78107953|gb|DV526371.1|DV526371
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|60352542|gb|DN219515.1|DN219515
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|148949106|gb|EC894535.2|EC894535
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATAT-TTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|149085023|gb|EE174532.2|EE174532
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|113702665|gb|EE680169.1|EE680169
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCTCCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|9730867|gb|BE509619.1|BE509619
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|37395454|gb|CF635007.1|CF635007
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|60342148|gb|DN209121.1|DN209121
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|60342166|gb|DN209139.1|DN209139
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|88746930|gb|DY531071.1|DY531071
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCGCCGAGGTTCTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|148942651|gb|EC887670.2|EC887670
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCCCCGAGGTTTTGGGTTTGTCCCCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|211424816|gb|FL445164.1|FL445164
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|211138006|gb|FL213711.1|FL213711
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|32864876|gb|CF004558.1|CF004558
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
EST: gi|40336792|gb|CK370862.1|CK370862
EST:     GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAG                         GACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT
genomic: GGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGAT

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: 208

GAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACAGATGATCTAAGGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGATGGTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCC


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 128

GAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACAGATGATCTAAGGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGATGGTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCC


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

GAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACAGATGATCTAAGGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGATGGTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCC


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 103

GAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACAGATGATCTAAGGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaa ... ttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGATGGTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttggcataccacaatatattagatgtcttaactcttcgaatttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGATGGTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCC
                             tcttaac  putative branch site (score: 103)
                                            tttctgt  putative PPT
              acaatatattagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcggctaagactggcattgtttggcataccacaatatattagatgtcttaactcttcgaatttctgtacagGACCCCAAAAGAAGCGGCCACCGAGGTTTTGGGTTTGTCACCTTCGCTGATGATGGTGTGGCAGAACGAGTAGCTCGTAGAAGCCATGAAATTCTAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC