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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggttttcctcacaccactacctgaggccgatctctccttcctcgagtgctcgcgaatgtctctgaaaaactcactgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGA

Basic information

species Zea mays
transcript GRMZM2G047143_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047143_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g40940.2 (Oryza sativa), 3'ss of exon 2
---------------------------------gtcggttttcctcacaccactacctgaggccgatctctccttcctcgagtgctcgcgaatgtctctgaaaaactcactgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGA
                                 | | || | | |       ||   |        | |  |       || || ||  |  ||| | |       |  |   |||||| |||||||||||||||||||||||| | ||||||||||| || |||||||| ||||||  ||||||||| ||||| |||||||||| ||||   |||||
gtcgtctggcctcactcaccggatcactagcctgcctgtctccatttggtttcttttttctttttcttttgctgctgctgattgatcttgcctgtgtttcctgcgttgccgcgcgcagAGTGGCTGGAGGCCGGGAAGCTGCAGAGGATCGTGCTGGTGATCATGAGCAAGGCCACCTCCGAGGTGCTGGAGCGGTGGAACTTCAGCATCCAGACCGA
















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|31406271|gb|CD485003.1|CD485003
EST:     GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAG                         AATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
genomic: GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
EST: gi|76019513|gb|DT946683.1|DT946683
EST:     CCTCCCAGCTTTCAG                         AATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
genomic: CCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
EST: gi|101396573|gb|EB820212.1|EB820212
EST:     GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAG                         AATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
genomic: GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
EST: gi|31441067|gb|CD510498.1|CD510498
EST:     GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAG                         AATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
genomic: GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
EST: gi|211437588|gb|FL436643.1|FL436643
EST:     GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAG                         AATGGCTGGAGGCCGGGAAGCTGCAGCGGATCGTGCTGGTCATAATGAGCA
genomic: GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
EST: gi|148946894|gb|EC892174.2|EC892174
EST:     GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAG                         AATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
genomic: GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
EST: gi|78078551|gb|DV506963.1|DV506963
EST:     GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAG                         AATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
genomic: GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
EST: gi|60349178|gb|DN216151.1|DN216151
EST:     GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAG                         AATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
genomic: GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
EST: gi|94475186|gb|EB704144.1|EB704144
EST:     GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAG                         AATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
genomic: GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
EST: gi|78023687|gb|DV492074.1|DV492074
EST:     CCTCACTTCCCAGCTTTCAG                         AATGGCTGGAGGCCGGGAAGTTGCAGCGGATCGTGCTGGTCATAATGAGCA
genomic: CCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA
EST: gi|32912163|gb|CF016975.1|CF016975
EST:     GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAG                         AATGGCTGGAGGCCGGGAAGCTGCAGCGGATCGTGCTGGTCATAATGAGCA
genomic: GGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCA

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: 153

GAGAGCTTCAGCAAGGTGAAGAAGTACGGGCTTACCATGCTGCTCACGCAGGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 15

GAGAGCTTCAGCAAGGTGAAGAAGTACGGGCTTACCATGCTGCTCACGCAGGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 22

GAGAGCTTCAGCAAGGTGAAGAAGTACGGGCTTACCATGCTGCTCACGCAGGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 22

GAGAGCTTCAGCAAGGTGAAGAAGTACGGGCTTACCATGCTGCTCACGCAGGACGAGGGCGTGAAGAACTTCATCGCCAGCCTCACCTCCCAGCTCTCAGgtcggttttc ... actgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatctctccttcctcgagtgctcgcgaatgtctctgaaaaactcactgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGA
                                        aactcac  putative branch site (score: 22)
                                   tgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggttttcctcacaccactacctgaggccgatctctccttcctcgagtgctcgcgaatgtctctgaaaaactcactgtcgcagAATGGCTGGAGGCCGGGAAGCTGCAGCGTATCGTGCTGGTCATAATGAGCAAAGCCACCAGCGAGGTGCTCGAGCGCTGGAACTTCAACATCGTCACCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA