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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagttctctgtctcttacccttcattagtatctcatattctcatgtaccatttgatgtctcatatcctagactaaatattaaaatgttttgtgtt...

Basic information

species Zea mays
transcript GRMZM2G484880_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G484880_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g34300.2 (Oryza sativa), 5'ss of exon 7
GGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagttctctgtctcttacccttcattagtatctcatattctcatgtaccatttgatgtctcatatcctagactaaatatta-aaatgttttgtgtt--
 |||| || ||||||  | |||||  |  |||  || |||||||   | || || ||||||||||| ||||||||||||||||| |||||| ||||||||||||| |  ||| |  | || | |  || ||  | | |  |||   ||  |  ||       |     |      | | ||||||     ||  |||   |  
AGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCAACGCTAAAAAAGCAACTTGTTGATGATTGGGAGTTTGTCACGCAGCTGGGTAAGgtattcaaatcttt--ccctgagctgtctttgatttatt-tatgtccaaatcacaaccttcattgttcaattataattgaatattgtgtctgagttggcatgg

upper sequence: GRMZM2G484880_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os11g34300.3 (Oryza sativa), 5'ss of exon 4
-----GGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagttctctgtctcttacccttcattagtatctcatattctcatgtaccatttgatgtctcatatcctagactaaatattaaaatgttttgtgtt--
      |||| || ||||||  | |||||  |  |||  || |||||||   | || || ||||||||||| ||||||||||||||||| |||||| ||||||||||||| |  ||| |  | || | |  || ||  | | |  |||   ||  |  ||       |     |      | | ||||||       | || |||  
GAGAAAGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCAACGCTAAAAAAGCAACTTGTTGATGATTGGGAGTTTGTCACGCAGCTGGgtaaggtattcaaatcttt--ccctgagctgtctttgatttatt-tatgtccaaatcacaaccttcattgttcaattataattgaatattgtg----tctgagttgg

upper sequence: GRMZM2G484880_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os04g01130.1 (Oryza sativa), 5'ss of exon 6
GGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagttctctgtctcttacccttcattagtatctcatattctcatgtaccatttgatgtctcatatcctagactaaatattaaaa-tgttttgtgtt--
 |||| || ||||||  | |||||  |  |||  || |||||||   |||| || || |||||||| ||||||||||||||||| |||||| ||||||||||||| | |||| |  |||| | || || ||   ||    |||   ||     || |     |     |      | | ||||||     ||  |||   |  
AGAAAGAAAATCATCTGAGAGTCTCTTCATGTCACATTTTCCTTCAACACTAAAAAAACAACTTGTTGATGATTGGGAGTTTGTCACGCAGCTGGGTAAGgtattcaattcttt--ctctgagccgtctttga-attatttatgtccaaagcacactcctcattgttcaattataattgaatattgtctctgaattggcatgg

upper sequence: GRMZM2G484880_T01 (Zea mays), 5'ss of exon 7
lower sequence: Vv07s0129g01020.t01 (Vitis vinifera), 5'ss of exon 7
GGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagttctctgtctcttacccttcattagtatctcatattctcatgtaccatttgatgtctcata----tcctagactaaatattaaaatgttttgtgtt
||| ||   |||| || | |  ||  |   | | |   ||||   | |||| |||||||||||||| ||||||||||| |||||||| |||  || ||||||| ||| |  ||    |   |  ||   |  || |  || |    || | |     |||||  | | |    |  |||    |||     |    |       
GGACAATGCATCAACAGAAAAGCTTGTCAAGATCCCAATTCCAGCGACACTAAAGAAGCAACTTGTTGATGATTGGGATTTTGTTACTCAGCAGGATAAGgtactta-tattccagtttagaatctgtgtgtgtgtggcacacaaacagg-atttgatgatgcttaaaaatagttttagttggaatggagcagaagtagaaa--

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|22546503|gb|BU098814.1|BU098814
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|93284202|gb|EB676466.1|EB676466
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|31997933|gb|CD661838.1|CD661838
EST:     TACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|60358481|gb|DN225454.1|DN225454
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGAT--G---G                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|60343282|gb|DN210255.1|DN210255
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|37386752|gb|CF630565.1|CF630565
EST:     AAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGAT--G---G                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: AAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|33095255|gb|CF055249.1|CF055249
EST:     TGAAGAAGCAACATGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTA
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTA
EST: gi|76016791|gb|DT943961.1|DT943961
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|78544095|gb|DV621593.1|DV621593
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|6031476|gb|AW076378.1|AW076378
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCT-CCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|32855367|gb|CD995048.1|CD995048
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAA
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAA
EST: gi|76912438|gb|DV164732.1|DV164732
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|26456042|gb|CA827625.1|CA827625
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGAT
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGAT
EST: gi|71331879|gb|DR802817.1|DR802817
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
EST: gi|71438521|gb|DR819571.1|DR819571
EST:     TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAG                         CTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC
genomic: TGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTAC

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: 49 (upstream exon), 48 (downstream exon)
Score: 234

GGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 71

GGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 90

GGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 92

GGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagtt ... tggcctgcagCTTGTGAAGCTACCACGATCACCTACTGTTGATGATATTCTAAAGAAGTACTTGGAACACCGGGCAAAGAAGGATGGCAA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGCAGATGGGTAAGgtatttagttctctgtctcttacccttcattagtatctcatattctcatgtaccatttgatgtctcatatcctagactaaatattaaaatgttttgtgtt

- - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG