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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttcccatccattacagtgttgcattaagataatttgggaatataatgaaaagagcgttctgattgaaaatggcacggagattcagagaggctgtgttgattgatgacagtcattgttttttgatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG

Basic information

species Zea mays
transcript GRMZM2G136803_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136803_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 3'ss of exon 20
gtgcgttcccatcca--ttacagtgttgcattaagataatt--tgggaatataatgaaaagagcgttctgattgaaaatggcacggagattcagagaggctgtgttgattgatgacagtcattgttttttgatgttt-cagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG
||||||| || | |   ||||   | | || || | | |||  |    ||  |   | |     ||| |   ||  ||    |    | ||  |||| ||| |   | ||||||       |||| |  |  | ||| |||||||||||||| ||||||||||| ||||| |||||||||||||||||||||||||||| |||||||||||| ||||||||| |||||||| |||| ||||
gtgcgtttcccttctgtttacttgggttcaatatgttcattgctacagatgcacacatacttaggttgtatatggcaaactaaaaatggtttggagaagctattcagtttgatgttcaattttgtgtcatatttttttcagGTTTGTGCTCCGTCATGTCATGATTGCTCCACATTACGTGCTTGGTGGGAAGAAGATGGAGGAAGAAGAAGCCGTTTCTACCAGACTGTAATTGGTAGTG

upper sequence: GRMZM2G136803_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA19G30580.1 (Glycine max), 3'ss of exon 21
gtgcgttcccatccattacagtgttgcattaagataatttgggaatataatgaaaagagcgttctgattgaaaa-tggcacggagattcaga---gaggctgtgttgattgatgacagtcattgttttttgatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG
                                     | |   |   |||     ||  | |  | ||||| || |          ||   |   |  ||| | ||| |||||    || |   |      ||||  ||||| ||||| || |||||||||||||| || || || ||||||||||||||||||||||||| |||||||   || || | ||||| |||  | |     |
-------------------------------------tataatatgctaaatctgagtccatcttcattgagaactaatgtaagtttttctatttggagctcttttgtttgat--tggttaacttgaggcaatgtg-cagGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACTCCGGTTTTTCAAGAATGTGATGGAGTCCG

upper sequence: GRMZM2G136803_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA03G27600.1 (Glycine max), 3'ss of exon 20
gtgcgttcccatccattacagtgttgcattaagataatttgggaatataatgaaaagagcgttctgattgaaaa-tggcacggagattcaga---gaggctgtgttgattgatgacagtcattgttttttgatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG
                                     | |   |   |||    |||  | |  | ||||| || |    |     ||   |   |  |   | ||| |||||    || | | |      ||||  ||||| ||||| || |||||||||||||| || || || ||||||||||||||||||||||||| |||||||    | || | ||||| |||  | |     |
-------------------------------------tataatatgctaaatctaagttcatctttattgagaactaatgcaagtttttctatttggagggcttttgtttgattg-ggtgact-taaggcaatgtg-cagGTATGTGCCCCTTCATGTCATGACTGTTCCACCTTGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACTCAGGTTTTTCAAGAATGTGATGGAGTCCG

upper sequence: GRMZM2G136803_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv08s0040g00670.t01 (Vitis vinifera), 3'ss of exon 19
gtgcgttcccatccattacagtgttgcattaagataatttgggaatataatgaaaagagcgttctgattgaaaa-tggcacggagattcagagaggctgtgttgattgatgacagtcattgttttttgatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG
                                |    |||   | | |  |        | |  | ||||||   |  ||       ||| |   | | ||||||      | || | |   |   |    |||||||| |||||||| ||||| |||||||| || ||  | ||||||||||||||||||||||||| ||||||| | || || |  |||||||| || ||   ||
------------------------------gggtaggttttccatttttgtttttctctcctggttattgaatccttacatcacatgtcacaatagttttgttga------ataggc-taactgaataccatttcagGTGTGTGCTCCATCATGCCATGACTGTTCCACCATGCGTGCTTGGTGGGAAGAAGATGAAGAAAGAAGACGACGATTTTTTAAGACTGTGGTAGGGTCTG

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|32932784|gb|CF037596.1|CF037596
EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
EST: gi|32930716|gb|CF035528.1|CF035528
EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTTTACATTACGTGCTTGGTGGGAA
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
EST: gi|32931864|gb|CF036676.1|CF036676
EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTTTACATTACGTGCTTGGTGGGAA
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
EST: gi|16927586|gb|BM080655.1|BM080655
EST:     TGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
genomic: TGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
EST: gi|32867796|gb|CF007478.1|CF007478
EST:     AACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
genomic: AACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
EST: gi|32932809|gb|CF037621.1|CF037621
EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
EST: gi|32837361|gb|CD977039.1|CD977039
EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAA
EST: gi|32836690|gb|CD976368.1|CD976368
EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGC
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGC
EST: gi|32932023|gb|CF036835.1|CF036835
EST:     GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACG                         GTTTGTGCTCCCTCATGTCATGACTGC-CTTACATTACGTGCTTGGTGGGA
genomic: GTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCT-ACATTACGTGCTTGGTGGGA

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: 46 (upstream exon), 48 (downstream exon)
Score: 42

GTTATGCAAGAACTGGGGTTGATTGGATTGCGTATCCAAAGAATGCCTAGTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

GTTATGCAAGAACTGGGGTTGATTGGATTGCGTATCCAAAGAATGCCTAGTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 36

GTTATGCAAGAACTGGGGTTGATTGGATTGCGTATCCAAAGAATGCCTAGTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 160

GTTATGCAAGAACTGGGGTTGATTGGATTGCGTATCCAAAGAATGCCTAGTGAACCAAACTTGGAATTTGGTATTCCTTCTCAGTATAGCTATATGACGgtgcgttccc ... gatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagattcagagaggctgtgttgattgatgacagtcattgttttttgatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG
                                         ttttgat  putative branch site (score: 160)
                                       ttttttg  CT-rich tract
                                   attgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgttcccatccattacagtgttgcattaagataatttgggaatataatgaaaagagcgttctgattgaaaatggcacggagattcagagaggctgtgttgattgatgacagtcattgttttttgatgtttcagGTTTGTGCTCCCTCATGTCATGACTGCTCTACATTACGTGCTTGGTGGGAAGAAGATGAAGGAAGAAGAAGTCGTTTCTACAAGACTGTAGTTGGCAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT