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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggaactgaagctgaagtgctgaaataatcctgtattttatatttgtattttacttggttcaaatcatgcaggtatgtgaatgtatggtttctgaattctaagctttggtggtgaatcttcatctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC

Basic information

species Zea mays
transcript GRMZM2G008611_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 5
gtttggaactgaagctgaagtgctgaaataatcctgtattttatatttgtattttacttggttcaaatcatgcaggtatgtgaatgtatggtttctgaattctaagctttggtggtgaatcttcatctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC
             | ||     |||||| | |  |  || || | |||| | ||   ||| |    |   |    |||  ||    | ||  || | ||   | ||||||| || ||  | |||||   |||||| |||||||||||||||||||| ||||||||||||||||| || |||||| |||||||||| |||||| |||| |   | | ||||||
-------------gttggga-actgaaaaactgttaaatgttct-tttgcaatta--ttgttctgtactgtctgtgtacatgtgaatctgagttattaaaattgagctttgctgatgtctgttcattcttgcagGCCATTTTAATATTTTTGTTGGCGATCTTTGCCCGGAAGTAACAGATGCTGCTTTGTTTGCTTTTTTCGCTGGATTTACCAGTTGCTC

upper sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 5
gtttggaactgaagctgaagtgctgaaataatcctgtattttatatttgtattttacttggttcaaatcatgcaggtatgtgaatgtatggtttctgaattctaagctttggtggtgaatcttcatct-----atgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC
                     |   | ||| |  | ||||||   |   | |||| ||      || |  | |||  || |   |||    ||||   |||  || |  || |  | || ||||||||     ||||||||||||  |||||||||||||| |||||| |||| || || || ||||||||  ||||||||| |||||||| |||  |||  || ||
---------------------gtatatatatttgtttattttg-gtacatttttttctgaa---aattggtccagtaatttccctgttccttttc---attacaaac--tgattatcaaacttcatctttggcatgcagGTCATTACAATATTTTTGTTGGTGATCTTAGCCCTGAGGTTACAGATGCTACACTGTTTGCATGTTTCTCTGTTTATCCTAGCTGTTC

upper sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 5
gtttggaactgaagctgaagtgctgaaataatcctgtattttatatttgtattttacttggttcaaatcatgcaggtatgtgaatgtatggtttctga-attctaagctttggtggtgaatcttcatctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC
||| |   ||| || | || |      ||||   |   | ||||  | | |    |  || |||     ||| || | || | ||  ||  ||  |||  || ||  |||   || ||          | || |||||| || || ||||||||||| |||||  |||| || || ||||||||||| ||||||||||  || |||| ||   | | ||| ||
gttggtttctgtagtttaattctatgcataagtttcactcttatgct-gca----aactgattc----tatggagttttg-gcattcatcattgttgatgttgtattcttgtatgatg---------ttgtgtagGTCACTTCAACATTTTTGTTGGTGATCTCAGCCCTGAGGTTACTGATGCTACATTGTTTGCATGCTTTTCTGTTTTTCCCAGTTGTTC

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|32927422|gb|CF032234.1|CF032234
EST:     ACTCCGAGGGAGGGCACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: ACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|32940921|gb|CF045740.1|CF045740
EST:     TACTCCGAGGGAGGGCACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: TACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|32927656|gb|CF032468.1|CF032468
EST:     ACTCCGAGGGAGGGCACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: ACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|32927013|gb|CF031825.1|CF031825
EST:     ACTCCGAGGGAGGGCACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: ACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|32850873|gb|CD990554.1|CD990554
EST:     GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGGCACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|32850928|gb|CD990609.1|CD990609
EST:     GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGGCACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|6270004|gb|AW157975.1|AW157975
EST:     GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|32927394|gb|CF032206.1|CF032206
EST:     GTACTCCGAGGGAGGGCACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GTACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|32928740|gb|CF033552.1|CF033552
EST:     ACTCCGAGGGAGGGCACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: ACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|33092403|gb|CF052397.1|CF052397
EST:     GTACTCCGAGGGAGGGCACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GTACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|32846545|gb|CD986226.1|CD986226
EST:     ACTCCGAGGGAGGGCACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: ACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|211381738|gb|FL482095.1|FL482095
EST:     GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGGCACATCAG                         GTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: GATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
EST: gi|32928010|gb|CF032822.1|CF032822
EST:     TACTCCGAGGGAGGGCACATCAG                         GTCATTTTAATATTTTTGGTGGGGATCTTTGCCCGGAAGTCACTGATGCTA
genomic: TACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTA

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: 35 (upstream exon), 49 (downstream exon)
Score: 77

GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 114

GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 73

GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

GTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGGCACATCAGgtttggaact ... atctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaatgtatggtttctgaattctaagctttggtggtgaatcttcatctatgcagGTCATTTTAATATTTTTGTTGGGGATCTTTGCCCGGAAGTCACTGATGCTACTTTGTTTGCATTTTTCTCTGGTTACTCTACTTGCTC
                                        tcttcatct  CT-rich tract
                  aattctaa  TA-rich tract