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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT

Basic information

species Zea mays
transcript GRMZM2G038848_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g42110.1 (Oryza sativa), 3'ss of exon 13
gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT
||||||| |||   ||| ||  ||    |  ||| ||  | |||   |||| ||| | | || ||||||| |   | | ||     | | |||||||| ||||||||||||||||||||||||||||||| ||||||||| | || || ||||||||||||||||| ||||| ||||| |  ||||||||||| || ||||| |
gtaagtgtctt---tcatctacatgtttctcaagcatttagcaatc-taatgtcatagacttcagatgcata---atcctatttcttgt-tttcaacaatgcagATAGATAATCTTGTGAAGGGAGCATCAGGTCAGGCTGTTCAGAACCTTAATCTGATGATGGGTCTGCCAGAGAACACTGGGCTGCAATATCAACCCCTAT

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os10g35170.1 (Oryza sativa), 3'ss of exon 13
gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagct-atgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT
||| | | |||||  || |||||| || |||         |||||  || | ||     | | | |    |  |   ||||    ||  |  ||||||    |||||||||||||||||||||||||| |||||||||||| | || || || |||||||||||||| ||||||||||| |  ||||||||||| |||||||| |
gtatgcgtcttcaaccatctttatgcc-cat-------tgtcaaac-tagtttcttcagacttaaagatgcgaaattcttattttcttgttcttcaactccacagATAGATAATCTTGTGAAGGGAGCGTCTGGTCAGGCTGTCCAGAACCTCAATCTGATGATGGGCCTGCCTGAGAACAGAGGGCTGCAATATCAGCCCCTAT

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA20G01220.1 (Glycine max), 3'ss of exon 12
------gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT
       | | |   ||   ||   | |||||  |  || | ||  |    ||| |||| |    ||||   |  |||| |||  ||       || |      |||||||| |||||| | ||||||||||| || ||||| ||||| ||||| |||||| || | |||||| | || || ||| |||| || || |||| ||| || |
gtatgttttaattttttttctcctatatatccagctgaaat-tgtgtatttaatgatattatgatattattgttgacat-gactctaagtatgttgatgtgttgttgcagATTGATAATTTAGTGAAGGGAGCTTCAGGTCAAGCTTTACAAAACCTTAATTTGTTAATGGGATTTCCAGAAAATTTGGGACTTCATTACCTGCCTCTTT

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA07G29630.1 (Glycine max), 3'ss of exon 13
gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatc----acataattaagatgca--catagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT
    ||   || |||    ||| | || | ||  ||| || |  ||||  | |     |    |||| ||| |     | ||| | || |  | || |      |||||||| |||||||| ||||||||||| || ||||| ||||| ||||| |||||| || | |||||| | || || ||| |||| || || |||| ||| || |
----gtatgttaagtt--tttttttcctcctatatatccagctgaaattgtgtatttaatgatattatgatactattgttgacatcactatgt-tgatgtgttgttgcagATTGATAATCTAGTGAAGGGAGCTTCAGGTCAAGCTTTACAAAACCTTAATTTGTTAATGGGATTTCCAGAAAATTTGGGACTTCATTACCTGCCTCTTT

upper sequence: GRMZM2G038848_T02 (Zea mays), 3'ss of exon 13
lower sequence: Vv03s0063g01110.t01 (Vitis vinifera), 3'ss of exon 12
------gtaagtgccttcagtcaactttatcccacataagtatgcatcaaaaataatatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT
       ||| |  | |  ||  |  || |   |       ||   || |  || | |    || | |||       ||         | |       ||     ||||||| |||||||||||||||||||| |||||||| || ||||| ||||||||| ||||||||||| |||| |||||||  || || |  ||||||||  |||
gtatgtttaaatttcctttgttcatgttttagaattccttcatatttctagtatgaaaggttattaataatcctactatcactggctaaggtctcaaatccttgctgcagATTGATAATCTTGTGAAGGGAGCTTCTGGTCAAGCCTTGCAGAATCTTAATGTGATGATGGGATTGCCGGAGAATACAGGACTTCTCTACCAGCCATTGT

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|30705886|gb|CD058958.1|CD058958
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|37397485|gb|CF636042.1|CF636042
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|6448353|gb|AW181119.1|AW181119
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|88747566|gb|DY531707.1|DY531707
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATTTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|32931445|gb|CF036257.1|CF036257
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|110202395|gb|EC884292.1|EC884292
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|32912849|gb|CF017661.1|CF017661
EST:     GGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: GGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|32930019|gb|CF034831.1|CF034831
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|71762552|gb|DR960489.1|DR960489
EST:     TGAATGTTTATGAGGATAGAATACCTGGAAGGGCCATCATCATTTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATTTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|148958090|gb|EC904281.2|EC904281
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|74234670|gb|DT642584.1|DT642584
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|60394782|gb|DN227652.1|DN227652
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|87155331|gb|DY400120.1|DY400120
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|26558690|gb|CA830925.1|CA830925
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|33093061|gb|CF053055.1|CF053055
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|60337236|gb|DN204209.1|DN204209
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|148942778|gb|EC887805.2|EC887805
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|19437017|gb|BM953427.1|BM953427
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|32931562|gb|CF036374.1|CF036374
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|40337039|gb|CK371109.1|CK371109
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|78080159|gb|DV508571.1|DV508571
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATTTTTGTC                         ATAGATAATTTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|22473066|gb|BU037546.1|BU037546
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|5706123|gb|AI941899.1|AI941899
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAG
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAG
EST: gi|211026572|gb|FL468584.1|FL468584
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|78079273|gb|DV507685.1|DV507685
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|148943027|gb|EC888077.2|EC888077
EST:     TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATTTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: TGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
EST: gi|67010559|gb|CO439308.1|CO439308
EST:     GAATGTCTATGAGGATAGAATACCTGGANAGG-CCATCATCATCTCTGTC                         ATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT
genomic: GAATGTCTATGAGGATAGAATACCTGGA-AGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 142

TAGCAATGTTCCTTGCACAAGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT


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

TAGCAATGTTCCTTGCACAAGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 126

TAGCAATGTTCCTTGCACAAGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 101

TAGCAATGTTCCTTGCACAAGCCATGTTGTGGGATCAAATTACTGCTTCATGAATGTCTATGAGGATAGAATACCTGGAAGGGCCATCATCATCTCTGTCgtaagtgcct ... aacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcacataattaagatgcacatagaccttacaagctatgtttcaacattgcagATAGATAATCTTGTGAAGGGAGCATCTGGTCAGGCTTTGCAAAATCTTAATCTGATGATGGGACTGCCTGAGAATATGGGGCTGCAATACCAGCCCCTGT
                          accttac  putative branch site (score: 101)
       ataattaagat  TA-rich tract