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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtcaaatctgaacacagcaaacctatttctggttgattcaatgagttacatatttcttgtcctttcag

Basic information

species Zea mays
transcript GRMZM2G174204_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174204_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 5'ss of exon 5
GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtcaaatctga-----------acacagcaaacc----tatttctggttgattcaatgagttacatatttcttgtcctttcag
                               || |||||||||||||| ||||||||||||| ||||||||||||||||||||| |||||  ||||||||||| || ||||  |  |           ||   |||| |     | || ||   |     ||  | |  || | || |  |||||||||
-------------------------------GTTCTCAGCAACACAATTAAGCAAAAGAGGATGGAAAAGGCTGGCAAATGGGAGGTTCCTTTGCCAAAGgtgattttcaacacaaactgtttctagtacctggcaatcaatggttttcctaccttgactaagcactgtcacaattttcttcctttcag

upper sequence: GRMZM2G174204_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 5
GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtg----tttgtcaaat-ctgaacacagcaaacctatttctggttgattcaatgagttacatatttct-tgtcctttcag-------------------------------------------------------------------------
                               || || ||||||||||| ||||||||||||||||| ||||| || |||||||||||||| || || ||||||    |  ||  ||| ||     ||  |     | |  |   |  | ||||| ||  | |||| || | || | |  |                                                                         
-------------------------------GTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattacgttcaatactttgtgcattatgttaaatgatatcttttgcaatgtgtatcttattgctatttcatgtttgttttatgtttccctgtgaatggaagggagcgaacttggtaattaaatgaatgtatgctttctcatttcttcag

upper sequence: GRMZM2G174204_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA10G00490.1 (Glycine max), 5'ss of exon 5
GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtg----tttgtcaaat-ctgaacacagcaaacctatttc-tggttgattcaatgagttacatatttcttgtcctttcag------------------------------------------------------------------------------
                               || || |||||||| || ||||||||||||||||| ||||| || |||||||||||||| || || ||||||    |  ||  ||| ||     ||   |   | ||   || |   |      | ||  ||  || |||   | |||                                                                               
-------------------------------GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttgtgcattgattatgttaaatgatatgtcttgcaatttgtat-cttattgctatgtcatgtgtgttttatgtttccctgtgaatggaagggagtgaacttggtaattaaatgaatgtatgctttctcatttcttcag

upper sequence: GRMZM2G174204_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 5
GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtg----tttgtcaaat-----ctgaacacagcaaacctatttctggttgattcaatgagttacatatttcttgtcctttcag---------------------------------------------------------------------------
                               || || |||||||| || ||||||||||||||||| ||||| || |||||||||||||| || || ||||||    |  ||  |||      || ||  |  |     |    |   |  | ||||  ||| | | |||||  | | |                                                                               
-------------------------------GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttttgcacggattatgttaaacgatatctcttgcaatttgttccttgtttctatttcatgtgtgttttatgtttccctgttaatggaagggagcgagcttgagtaattaaatgaatgtatactttctcatttcttcag

upper sequence: GRMZM2G174204_T02 (Zea mays), 5'ss of exon 1
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtcaaatctgaacacagcaaacctatttctggttga--ttcaatgagtta--------catattt----cttgtcctttcag--
                               || || |||||||| || || ||||||||||| || || |||||||||||||| || || || |||||||||         |||   |      |  |  |   || ||||  |  ||  | |           | |||     | |||||||| |   
-------------------------------GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgcttttgtattccttcagtgtttgaactctaacaaatgggcaaagcttaaattcaagccctgtccttttacag

upper sequence: GRMZM2G174204_T02 (Zea mays), 5'ss of exon 1
lower sequence: EFJ15002 (Selaginella moellendorffii), 5'ss of exon 5
GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtcaaatctgaacacagcaaacctatttctggttgattcaatgagttacatatttcttgtcctttcag
                               || || |||||||  |||||||||||| | |||||||| || || |||||| | |||||||| ||||||||  | | |||   ||    |         ||   ||  |  ||| |                           
-------------------------------GTTCTGAGCAACAGTATCAAGCAAAAGCGTAAGGAAAAAGCAGGAAAATGGCAAGTTCCGCTTCCAAAGgtaatcg-caaccatgccttcgatctcatcatacatgtcttgttccag--------------------------

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|60340980|gb|DN207953.1|DN207953
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG                         GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
EST: gi|60354693|gb|DN221666.1|DN221666
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG                         GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
EST: gi|60347312|gb|DN214285.1|DN214285
EST:     CCGCTGCCAAAG                         GTCAGACCTGTTGTTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
genomic: CCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
EST: gi|50332540|gb|CO527666.1|CO527666
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG                         GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
EST: gi|45847152|gb|CN071095.1|CN071095
EST:     TGGCAAATGGGATGTTCCGCTGCCAAAG                         GTCAGACCTGTAGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
genomic: TGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
EST: gi|60350420|gb|DN217393.1|DN217393
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG                         GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
EST: gi|211296298|gb|FL480002.1|FL480002
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG                         GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
EST: gi|78109119|gb|DV527536.1|DV527536
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG                         GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
EST: gi|60353886|gb|DN220859.1|DN220859
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG                         GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
EST: gi|17930472|gb|BM267432.1|BM267432
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAG                         GTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAG

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), 49 (downstream exon)
Score: 282

GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 307

GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 98

GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtca ... gtcctttcagGTCAGACCTGTTGCTGAAGAAGAAATGTTCAAGGTGCTACGAACTGGCAAGCGAAAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATTGATCACTGATTTCTGGTGAAGCGTAGGTACTCAGCAACACAATCAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCGCTGCCAAAGgtgtttgtcaaatctgaacacagcaaacctatttctggttgattcaatgagttacatatttcttgtcctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA