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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTCATGGAAGTGCACTGGGTGCCAAAGAGGTTGAAGCAACCAGGCAGAACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctaccctttgttctagtaatctagttatctcaatgggtttgtcaaatgcatagcaatcatataatttccttgaatggatcattgcag

Basic information

species Zea mays
transcript GRMZM2G033208_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G033208_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 5'ss of exon 5
GTGTTCATGGAAGTGCACTGGGTGCCAAAGAGGTTGAAGCAACCAGGCAGAACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctaccctttgttctagtaatctagttatctcaatgggtttgtcaaatg-catagcaatca---tataatttccttgaatggatcattgcag
| || || ||||||||  ||||| ||||||||||||||||||||||  ||||||||||||||||||||||  |||||||||| || ||||| || |||||||| |||||    ||||| |     | | ||||||| |||| | |  | ||||  ||||||| |||   |||  |||  ||| ||||    || |||
GCGTCCACGGAAGTGCTTTGGGTACCAAAGAGGTTGAAGCAACCAGAGAGAACCTTGGATGGCCCTATGAGCCATTCTTTGTGCCTGAGGATGTGAAGAGgtttgtcta----ttgttgt-----tttggttatctgaatgagatgttgaaatttcatagcactcaccttatggtttatttgcatgggctgttacag

upper sequence: GRMZM2G033208_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA03G03200.1 (Glycine max), 5'ss of exon 5
GTGTTCATGGAAGTGCACTGGGTGCCAAAGAGGTTGAAGCAACCAGGCAGAACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctaccctttgttctagtaatctagttatctcaatgggtttgtcaaa-tgcatagcaatcatataatttccttgaatggatcattgcag
|||| |||||||||||||||||||||||||| ||||| || ||||||||||||||||||||| |  ||||  |||||   || || ||||| ||||| | ||  |  |     | | | |||  || |  || |  |  ||    ||   |  |  |||   ||  |  |      |||  ||  |     |||
GTGTGCATGGAAGTGCACTGGGTGCCAAAGAAGTTGATGCCACCAGGCAGAACCTTGGATGGTCACATGAGCCATTCCACGTGCCTGAGGATGTCAAAAAgtatggatga---tgggtttagagatttcttttttcctgtgacactgctgaggtttataatgatactgaataagaattgcttgtctgtccccag
















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|211471115|gb|FL255208.1|FL255208
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCAC
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCAC
EST: gi|7137734|gb|AW499243.1|AW499243
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
EST: gi|6952400|gb|AW424468.1|AW424468
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
EST: gi|71311290|gb|DR791959.1|DR791959
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
EST: gi|148999663|gb|EE036652.2|EE036652
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCCGA-GGTGCTGCACTTGAGGC
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCC-GAAGGTGCTGCACTTGAGGC
EST: gi|74242160|gb|DT650074.1|DT650074
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
EST: gi|78083891|gb|DV512284.1|DV512284
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
EST: gi|78079232|gb|DV507644.1|DV507644
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
EST: gi|31360105|gb|CD444462.1|CD444462
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAG
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
EST: gi|67017393|gb|CO446142.1|CO446142
EST:     AACCTTGGATGGCCCTACGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
EST: gi|9952380|gb|BE638963.1|BE638963
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
EST: gi|76281987|gb|DV021555.1|DV021555
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
EST: gi|67012406|gb|CO441155.1|CO441155
EST:     AACCTTGGATGGCCCTACGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
EST: gi|71435831|gb|DR816881.1|DR816881
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
EST: gi|76285425|gb|DV024993.1|DV024993
EST:     AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAG                         TCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA
genomic: AACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAA

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: 270

GTGTTCATGGAAGTGCACTGGGTGCCAAAGAGGTTGAAGCAACCAGGCAGAACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAACGCTAAGTTTGCAGAGTACGAGAAGAAGTATGCAGATGATGCAGCAACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1198

GTGTTCATGGAAGTGCACTGGGTGCCAAAGAGGTTGAAGCAACCAGGCAGAACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAACGCTAAGTTTGCAGAGTACGAGAAGAAGTATGCAGATGATGCAGCAACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 583

GTGTTCATGGAAGTGCACTGGGTGCCAAAGAGGTTGAAGCAACCAGGCAGAACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAACGCTAAGTTTGCAGAGTACGAGAAGAAGTATGCAGATGATGCAGCAACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1120

GTGTTCATGGAAGTGCACTGGGTGCCAAAGAGGTTGAAGCAACCAGGCAGAACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctac ... atcattgcagTCACTGGAGCCGCCACACACCCGAAGGTGCTGCACTTGAGGCTGATTGGAACGCTAAGTTTGCAGAGTACGAGAAGAAGTATGCAGATGATGCAGCAACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTCATGGAAGTGCACTGGGTGCCAAAGAGGTTGAAGCAACCAGGCAGAACCTTGGATGGCCCTATGACACATTCTTTGTACCAGAGGACGTCAAGAGgttggtctaccctttgttctagtaatctagttatctcaatgggtttgtcaaatgcatagcaatcatataatttccttgaatggatcattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA