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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaatttgacagtttagctgttgtactgttagagtgatcatcactagggtactaaatgacatacaaaattcattgctgccttatttttgtactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG

Basic information

species Zea mays
transcript GRMZM2G168252_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168252_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g43620.1 (Oryza sativa), 3'ss of exon 3
gtactaatttg-acagtttagctgttgtactgttagagtgatcatcactagggtactaaatgacatacaaaattcatt-gctgc--cttatttttgt-----actg--tgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG
||| |  ||||  |  | |  | |||  | |  |  |      | | ||    ||  ||   |||| | | ||||||| ||||    ||| |  |||     ||||  | ||||| || ||||| |||||||| |||||||| |||||||||||||||||||||||||| ||||| ||
gtattgttttgtgctttatttcagttaaattcgttcaccatctacc-ctttaatatgaatcaacatgccatattcatttgctgtaatttactcgtgtcccctactgctttcagCTGGCTAATACAGAGGAGTATATTGATGGACAATTCTCTGGAAACCTGGGAGAGATACTGATTAG

upper sequence: GRMZM2G168252_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g08090.2 (Oryza sativa), 3'ss of exon 4
gtactaatttgacagtttagctgttgtactgttagagtgatcatcactagggtactaaatgacatacaaaattcattgctgcct---tatttttgtactg--tgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG
||| || ||||    ||| |     ||    || |     | | || || ||  | |  || ||| |    ||   |||    |   || || | |||||  | ||||| || ||||| |||||||| |||||||||||||||||||||||| |||| ||||| ||||| ||
gtattattttgt--attttgtatcagttaaattcgttcatttaccaatatggatcgacgtgtcat-cttcttttgctgcaatttacctaattgtctactgctttcagCTGGCTAATACAGAGGAGTATATTGATGGGCAATTCTCTGGAAACTTGGGTGAGATACTGATAAG

upper sequence: GRMZM2G168252_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g08090.1 (Oryza sativa), 3'ss of exon 3
gtactaatttgacagtttagctgttgtactgttagagtgatcatcactagggtactaaatgacatacaaaattcattgc---tgccttatttttgtactg--tgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG
||| || ||||    ||| |     ||    || |     | | || || ||  | |  || ||| |    ||   |||   |  | || || | |||||  | ||||| || ||||| |||||||| |||||||||||||||||||||||| |||                
gtattattttgt--attttgtatcagttaaattcgttcatttaccaatatggatcgacgtgtcat-cttcttttgctgcaatttacctaattgtctactgctttcagCTGGCTAATACAGAGGAGTATATTGATGGGCAATTCTCTGGAAACTTGG----------------

upper sequence: GRMZM2G168252_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G14285.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------------------gtactaatttgacagtttagctgttgtactgttagagtgatcatcactagggtac-taaatgacatacaaaat----tcattgctgcctt--atttttgtactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG
                                                                         | | ||||| |  | ||||    | || | |||||||     | |    | ||| || ||    ||   | |    ||||||     ||  ||  ||||  | || |||| |  || || ||||| |||||||||||||||||  | |||||||| ||||||||| |||||||
gtatggtcttagcttctatgttcaactcaagatcatgttcttgtcattgaagttttaaacagagattgatgttttcaaatttcaatgcttagaaaatctattcttagagtctatgt-atagagatacatagatcgtttattcattgtagtcattgagattttccatgcttgttttttgtagCTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGAGAGATTTTGATCAG

upper sequence: GRMZM2G168252_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv00s0220g00030.t01 (Vitis vinifera), 3'ss of exon 3
-gtactaat-ttgacagtttagctgttgtactgttagagtgatcatcactagggtactaaatgacatacaaaattcattgctgccttatttttgtactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG
  |  |  |  |  ||   | |||| |   || |   |||| |  |   ||   |||| | ||       |  ||   |  | | |     |  |  | ||||||| ||||| | ||| || ||||||||||| || ||| |||||||||| ||||||||| |||||||
tttgtttctgctaccaaactggctgctaagctttgtcagtgtttgtgtata---tactga-tggttggtgatgtttcataattcatgggaatctttttctgcagCTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG

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|31405643|gb|CD484375.1|CD484375
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211141410|gb|FL260967.1|FL260967
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|32864163|gb|CF003845.1|CF003845
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|32859161|gb|CD998842.1|CD998842
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|28982615|gb|BQ539401.2|BQ539401
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211142842|gb|FL260983.1|FL260983
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|213173178|gb|FM191015.1|FM191015
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211144268|gb|FL260991.1|FL260991
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211141405|gb|FL260962.1|FL260962
EST:     GTTATCTTGCTTCGGTGGACTCCTATATGAATCTCCAG                         CTTGCCAACACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211144276|gb|FL260999.1|FL260999
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|33094679|gb|CF054673.1|CF054673
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|18163186|gb|BM333025.1|BM333025
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|32856286|gb|CD995967.1|CD995967
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|32935643|gb|CF040455.1|CF040455
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211142836|gb|FL260977.1|FL260977
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211142832|gb|FL260973.1|FL260973
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|9731866|gb|BE510618.1|BE510618
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|18170962|gb|BM340802.1|BM340802
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211141409|gb|FL260966.1|FL260966
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211142834|gb|FL260975.1|FL260975
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|32913432|gb|CF018244.1|CF018244
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211142846|gb|FL260987.1|FL260987
EST:     GTTATCTTGCTTCGGTGGACTCCTATATGAATCTCCAG                         CTTGCCAACACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211144275|gb|FL260998.1|FL260998
EST:     GTTATCTTGCTTCGGTGGACTCCTATATGAATCTCCAG                         CTTGCCAACACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211144269|gb|FL260992.1|FL260992
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211144267|gb|FL260990.1|FL260990
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211141413|gb|FL260970.1|FL260970
EST:     TTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211144272|gb|FL260995.1|FL260995
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|211142843|gb|FL260984.1|FL260984
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACAT-GATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|113605055|gb|DW772787.1|DW772787
EST:     GGTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GGTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|32945393|gb|CF050212.1|CF050212
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|31405642|gb|CD484374.1|CD484374
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|32935872|gb|CF040684.1|CF040684
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
EST: gi|16917997|gb|BM073532.1|BM073532
EST:     GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAG                         CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA
genomic: GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGA

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: 45 (upstream exon), 49 (downstream exon)
Score: 892

GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 396

GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 369

GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 312

GTTATCTTGCTTCAGTGGACTCCTATATGAATCTCCAGgtactaattt ... tactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagggtactaaatgacatacaaaattcattgctgccttatttttgtactgtgcagCTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAG
     tactaaa  putative branch site (score: 312)
                                       tttttgt  putative PPT
                atacaaaattcatt  TA-rich tract