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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgttgaacaatttgccatttttatcttataaaaattgagataggaagccaatttaattggaaattcattacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA

Basic information

species Zea mays
transcript GRMZM2G063492_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 6
-gtttgttgttgaacaatttgccatttttatcttataaaaattgagataggaagccaatttaattggaaattcattacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA
  |||    || ||  |  ||   ||  | |||| |||||  ||| | || |  ||| |  |  || || ||  ||||||||||||||||||||| || ||||||||||||||||||||||| |||||||||||||| ||||| |||||||| ||||||||||||||||| |||||||||||| 
gtttttccatttaatgacctgttgttaatgtcttgtaaaa--tgaaacagcacaccattaaatatgcaattttgttacttgcagGTGCTTAACCAAGACGAAACACCCCTACTCTATAGTCTGGTTTTTGGTGAAGGGGTTGTCAATGATGCTACATCTGTTGTGCTCTTTAATGCAATTGAAG

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 6
gtttgttgttgaacaattt-gccatttttatcttataaaaattgagataggaagccaatttaattggaaattcattacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA
|||||  |    | | |||    ||| ||   | |   ||  |   |  |  ||  |  | || |   || | || |  |||||||||| || |||||||| |||||  | || || ||||| || ||||| || |||||||| |||||||| ||||| || ||||| |||||||||||  |||
gtttgaagcaatatatttttaaaattcttccttcaactaaggtatcactgctagtta-ctgaacttataaatgatga--tgcagGTGCTAAATCAGGATGAGACACCTTTGCTGTACAGTCTTGTATTTGGGGAGGGTGTTGTGAATGATGCTACATCAGTGGTGCTTTTCAATGCAATCCAAA

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 5
gtttgttgttgaacaatttgccatttttatcttataaaaattgagat-aggaagccaat--ttaattggaaattcattact-----tgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA
    ||| | ||||||| ||    ||||  |  |        |  |  | |  | ||||  ||| |    || | || | |     |||||||||| ||||||||||| |||||  |||| || ||||| || ||||| || |||||||| |||||||| |||||||| ||||| |||||||||||  |||
----gtt-tggaacaatatgtgcctttttccgcaacgttgcagcaaccaaggtgtcaatgcttagtactgaacttataaatgatgttgcagGTGCTAAACCAGGATGAGACACCTTTACTGTACAGTCTTGTATTTGGCGAGGGTGTTGTGAATGATGCTACATCTGTGGTGCTTTTCAATGCAATCAAAA

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 5
gtttgttgttgaacaatttgccatttttatcttataaaaattgagataggaagccaat--ttaattggaaattcattact-----tgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA
    ||| | |||| || ||    ||||     ||  |     |   | |  | ||||  | | |    |||| || | |     |||||||||| ||||||||||| |||||  |||| || ||||| || ||||| || |||||||| |||||||| |||||||||||||| || ||||||||  |||
----gtt-tggaacgatatgtgcctttttcgcaatgtagcagcaacgaaggtgtcaatgctaagtactgaatttataaatgatgttgcagGTGCTAAACCAGGATGAGACACCTTTACTGTACAGTCTTGTATTTGGCGAGGGTGTTGTGAATGATGCTACATCTGTTGTGCTTTTTAATGCAATAAAAA

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA20G37370.1 (Glycine max), 3'ss of exon 6
gtttgttgttgaacaatttgccatttttatcttataaaaattgagataggaagccaatttaattggaaattcattacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA
|||||    |  |   |||   ||| ||   | |   ||  |   |  |  ||  |  | || |   || | || |  |||||||||| || |||||||| |||||  | || || ||||| || ||||| || |||||||| |||||||| ||||| || ||||| |||||||||||  |||
gtttgaaaatatattttttaa-attcttccttcaactaaggtatcactgctagtta-ctgaacttataaatgatga--tgcagGTGCTAAATCAGGATGAGACACCTTTGCTGTACAGTCTTGTATTTGGGGAGGGTGTTGTGAATGATGCTACATCAGTGGTGCTTTTCAATGCAATCCAAA

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G06370.1 (Arabidopsis thaliana), 3'ss of exon 6
-------gtttgttgttgaacaatttgccatttttatctta-taaaaattgagataggaagccaatttaattggaaattcattacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA
        ||| ||  ||||  |||      | ||||  || || |  ||   ||   ||   || ||    |    ||  |||  |  |||||||||| || || || ||||| ||  | || ||||| || ||||| |||||||| || || ||||||||||| || |||||||||||||||||  | |
gtaagaactttttttctgaaacattcaaagatattattctactacattttctaatcaaaaattaacttgcacg---ctttgttaaatctagGTGCTTAATCAAGACGAGACACCTCTCTTGTACAGTCTTGTCTTTGGAGAAGGTGTAGTGAACGATGCCACATCGGTCGTGCTCTTCAATGCAATACAGA

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 2
gtt-tgttgttgaacaatttgccatttttatcttataaaaattgagataggaagccaatttaattggaaat-tcattactt-------gcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA
||  |||  ||   ||||| ||       |    ||| |     |||    |||   | ||||    || | |  || |||        ||||| || || || ||||| |||||  | || || ||||| || ||||| || || ||||| |||||||||||||||||||||||||||||||| ||| | |
gtaatgtgattcgccaattagcag----aagtacatacaggcccagaatcaaagtgtaattaacaaaaactcttgttcctttggtgatacagGTTCTCAATCAAGATGAGACACCTTTGCTTTACAGTCTTGTATTTGGAGAGGGCGTTGTGAATGATGCCACATCTGTTGTGCTCTTCAATGCTATTCAGA

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 6
gtttgttgttgaac--aatttgccatttttatcttataaaaattgagataggaagc-----caatttaattggaaattcattacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA
   |   | ||  |  | |  ||  |  |  | |||  |    | ||  |  |  |     ||| ||| ||    | ||      ||||||||||||| |||||||| |||||| ||||||| ||||| |||||||| ||||||||||| ||||||||||||||||| ||||| |||||||||||  | |
--gtacagatggccttactaagctgtgatcctgttactagttctaagggacaacacttccacaacttatttatccaatccaattgtgcagGTGCTTAATCAGGATGAGACACCCTTACTCTACAGTCTGGTTTTTGGAGAAGGTGTTGTGAATGATGCCACATCTGTGGTGCTTTTCAATGCAATCCAGA

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 3'ss of exon 5
gtttgttgttgaacaat-ttgccatttttatcttataaaaattgagataggaagccaatttaattggaaattcattact-tgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA
|| || ||    ||||  ||         |    | ||   |    ||||      || | ||        |  | |   |||||||||||||||||||||| || ||  |||| ||||| || || ||||| || || ||||| ||||||||  |||| ||||| || |||||||||||  | |
gtatggtgcattacaaagttatagcagccagacaacaatggtaccaatagttgtgaaactaaaccttttccttctgatgatgcagGTGCTTAACCAGGATGAGACGCCTTTACTTTATAGCCTGGTCTTTGGGGAGGGGGTTGTAAATGATGCAGCATCAGTTGTTCTTTTCAATGCAATCCAGA

upper sequence: GRMZM2G063492_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 5
--gtttgttgttgaacaat-ttgccatttttatcttataaaaattgagataggaag---ccaatttaattggaaattcattacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA
   |   |   |   |||   ||  ||| |  |   ||||        |||| |     |  | | || |    ||    || | ||||||||| || |||||||| |||||  | || || |||||||| ||||| |||||||| || |||||||||||||||||                       
gtatagatatcttctcaaggctgtgattctgcttccataatggggacaatagaacatttctgactaaagtttgcatctgata-tggcagGTGCTCAATCAGGATGAGACACCTTTGCTATACAGTCTAGTCTTTGGGGAAGGTGTGGTAAATGATGCCACATCTGTG----------------------

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|18963600|gb|BM660526.1|BM660526
EST:     CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAG                         GTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAA
genomic: CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAGgtttgttgtt ... ttacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAA
EST: gi|71320091|gb|DR796800.1|DR796800
EST:     CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAG                         GTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAA
genomic: CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAGgtttgttgtt ... ttacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAA
EST: gi|78078433|gb|DV506847.1|DV506847
EST:     CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAG                         GTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAA
genomic: CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAGgtttgttgtt ... ttacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAA
EST: gi|67026824|gb|CO455573.1|CO455573
EST:     CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAG                         GTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAA
genomic: CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAGgtttgttgtt ... ttacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAA
EST: gi|91872698|gb|EB402655.1|EB402655
EST:     CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAG                         GTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAA
genomic: CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAGgtttgttgtt ... ttacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAA
EST: gi|78118702|gb|DV537086.1|DV537086
EST:     CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAG                         GTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAA
genomic: CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAGgtttgttgtt ... ttacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAA

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: 44 (upstream exon), 49 (downstream exon)
Score: 91

CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAGgtttgttgtt ... ttacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 219

CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAGgtttgttgtt ... ttacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAGgtttgttgtt ... ttacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 112

CAATTGGTGCTATTTTCTCGGCAACAGATTCTGTTTGCACCTTACAGgtttgttgtt ... ttacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttataaaaattgagataggaagccaatttaattggaaattcattacttgcagGTGCTTAACCAGGATGAAACACCCCTACTCTATAGTCTAGTTTTTGGTGAAGGTGTTGTTAATGATGCCACATCTGTTGTGCTCTTCAATGCAATTGAAA
                            atttaat  putative branch site (score: 112)
                           aatttaattggaaatt  TA-rich tract