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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttattttctctcttgaggcttgaagaccatcttaaccttttgaactttacatgtaggtggagaagactgagatcttatttattttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG

Basic information

species Zea mays
transcript GRMZM2G137528_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 4
gtttattttctctcttgaggcttgaagaccatcttaa-ccttttgaactttacatgtaggtggagaagactgagatcttatttattttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG
     |||   ||  | |      || | |||||||| |  |   |  ||||  | |  |  || || | | |       | | ||||||||||||||||| || ||||| ||||||||||||||||| |||||| |||||||||| |||||||||||||||||||||||||||||||||||||||||||| |
----gtttgaacttcttaac----aatatcatcttaaacgatcctatttttaagtattagcagaaaatattaac------tctcttttttcagGGTGTCCTTCTCTATGGCCCTCCAGGCACAGGAAAAACATTGTTGGCACGTGCAGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCCG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 4
gtttattttctctcttgaggcttgaagaccatcttaaccttttgaactttacatgtaggtggagaag---------actgagatcttatttattttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG
   || | |||   ||  || |||  |   |  ||   | ||  | |   |||  | | ||  ||            ||||     |   |    |  ||||||||||| || ||||| || || || |||||||| |||||| ||||  | || || |||||||| |||||||| || ||||||||||||||||||||||
--gtagtgtctgattttggggttgttgctaaattttgtcattccatcagcacacttggttgttgatttttctgtttgctgaatctcttgatcacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGAAAAACATTGTTGGCTAGGGCAGTGGCTCATCATACTGACTGTACATTCATCAGGGTGTCTGGTTCTG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 4
gtttattttctctcttgaggcttgaagaccatcttaaccttttgaactttacatgtaggtggagaagactgagat--cttatttattt-------tttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG
||   || ||  | | | |  |||   |   |  | |     | | |   |||  | | ||   |    |  | |  || | |   ||       |  ||||||||||| || ||||| || || || ||||| || |||||| ||||  | || || |||||||| |||||||| || ||||||||||||||||||||||
gtagtttctcattttggggtgttgctaaattttgtcattccatcagcagcacacttggttgtttatttttctgtttgctgagtctcttgaacacatcacagGGTGTCCTGCTCTATGGGCCACCTGGTACAGGTAAAACATTGTTGGCTAGGGCAGTGGCTCATCATACTGACTGTACATTCATCAGGGTGTCTGGTTCTG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 4
gtttattttctctcttgaggcttgaagaccatcttaaccttttgaactttacatgtaggtggagaagactgagatcttatttattttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG
          |   || ||   |         ||  | |||  | |   ||    |   |  |   || |  |||    ||  || |  ||||| ||||| || ||||| || || || ||||| || || ||||| ||| | || || |||||||| |||||||| || ||||||||||| ||||||||||
---------gtagttttagttgtagtattttgctggagcttaagtatcataagcttttattaatttgattttgat----ttctttataacagGGAGTCCTGCTGTATGGGCCACCTGGTACAGGGAAAACTTTGCTTGCAAGGGCAGTAGCTCATCATACTGACTGTACTTTCATCAGGGTTTCTGGTTCTG

upper sequence: GRMZM2G137528_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 4
gtttattttctctcttgaggcttgaagaccatcttaaccttttgaactttacatgtaggtggagaagactgagatcttat---ttattttttc--------agGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG
  |||||| |||  | |   |||  |     | | |     |  |||| |   || | ||    || |||  | ||| ||    |||||||          |||| ||||| |||||||| ||||| || ||||| || ||| | || ||| | || || ||||||||||||||||| ||||| || ||||| ||||| ||||
-gttatttcctccatagcaacttctaatttgtttgactagctgcaactgtt--tggaagtcattaaaactcggttctaatagtctatttttatgtgttaatagGGAGTCCTGCTTTATGGTCCTCCTGGTACAGGGAAAACACTTCTTGCAAGGGCAGTGGCTCATCACACTGACTGTACCTTTATAAGGGTTTCTGGCTCTG

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|32941875|gb|CF046694.1|CF046694
EST:     CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG                         GGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
genomic: CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
EST: gi|37393602|gb|CF634067.1|CF634067
EST:     AATCAAACATCCGGAAATATTTGAGAGCC-TGGAATTGCAC-ACCAAAAG                         GGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACG
genomic: AATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACC-AAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACG
EST: gi|6989624|gb|AW447837.1|AW447837
EST:     CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCACAACCAAAG                         GGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
genomic: CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
EST: gi|19350715|gb|BM895247.1|BM895247
EST:     CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG                         GGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
genomic: CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
EST: gi|211070411|gb|FL012986.1|FL012986
EST:     CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG                         GGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
genomic: CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
EST: gi|67024358|gb|CO453107.1|CO453107
EST:     CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG                         GGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
genomic: CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
EST: gi|19350732|gb|BM895264.1|BM895264
EST:     CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG                         GGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
genomic: CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
EST: gi|60395128|gb|DN227997.1|DN227997
EST:     CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG                         GGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
genomic: CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
EST: gi|60352642|gb|DN219615.1|DN219615
EST:     ATTGCCC-ACCAAAG                         GGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
genomic: ATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
EST: gi|32866277|gb|CF005959.1|CF005959
EST:     CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG                         GGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
genomic: CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
EST: gi|32933070|gb|CF037882.1|CF037882
EST:     CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAG                         GGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT
genomic: CAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGT

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: 256

GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 299

GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 195

GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 267

GTCATTGAGCTTCCAATCAAACATCCGGAACTATTTGAGAGCCTTGGAATTGCCCAACCAAAGgtttattttc ... attttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttgaactttacatgtaggtggagaagactgagatcttatttattttttcagGGTGTCCTCCTTTATGGACCTCCAGGCACAGGAAAGACATTGCTGGCACGTGCGGTTGCTCATCACACTGACTGCACCTTCATCAGGGTGTCTGGTTCTG
                                     tcttatttattttttc  CT-rich tract
                                  agatcttatttatttt  TA-rich tract