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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcctaaaatcttattgctctactacattttttgtgatatagttgtatttcgtatgaaattgctgacttattatttttaacttgtatgtgcatgcag

Basic information

species Zea mays
transcript GRMZM2G164562_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 5'ss of exon 10
GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcctaaaatcttattgctctac---tacattttttgtg-----------atatagttgtatttc------------------------gtatgaaattgctgacttattatttttaacttgtatgtgcatgcag
|||| ||||  ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| |||||||||| ||||||||||| |||||||| ||||||    | | ||| | |||   || ||| ||| |            || ||| || |||                          |||| | |  | || |||| ||||| |||  ||||||| |||||||
GTACTGACTACACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGAACAAGAACTAATCGTTCAGGCGGTGTGCAGgtttt-atcctagtcccctgttgttttacagttatattatttattgttttcgctacatctagctgcattctagattaaaaaaatactagtaaatagtataacaccgttgtcttagtatttataatgtgtatgtccatgcag

upper sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA10G35560.2 (Glycine max), 5'ss of exon 10
GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcctaaaatcttattgctctactacattttttgtgatata-gttgtatt--tcgtatgaaattgctgacttattatttttaacttgtatgtgcatgcag
| ||    || ||||| ||||| |||||||||||||||||||| |||||   ||||||    || ||| |||| |||||||| || ||  | ||||| ||| | ||    | | ||| ||  | ||  | |||   |||||    | |||   ||  |||    |  |   ||    | | | |  |||||   ||  |||
GCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAGgtatttgtgctgttctgtaattacta-attagttgtttctagatatgcactatatcagtcacatgtctatatttgttttacttatattatctgtattgacaatcag
















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|211540750|gb|FL105308.1|FL105308
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|211540751|gb|FL105309.1|FL105309
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|60357187|gb|DN224160.1|DN224160
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|78089033|gb|DV517426.1|DV517426
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|32862616|gb|CF002298.1|CF002298
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|7216715|gb|AW562837.1|AW562837
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|40335508|gb|CK369578.1|CK369578
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|213172541|gb|FM189510.1|FM189510
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|32808278|gb|CD960512.1|CD960512
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCCTTTA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTA
EST: gi|211540748|gb|FL105306.1|FL105306
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|113701263|gb|EE678767.1|EE678767
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|32808708|gb|CD960942.1|CD960942
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCCTTTA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTA
EST: gi|32834558|gb|CD974236.1|CD974236
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|211229044|gb|FL456611.1|FL456611
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|32944234|gb|CF049053.1|CF049053
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|60337133|gb|DN204106.1|DN204106
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|18659504|gb|BM500373.1|BM500373
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCCAAAGTGGCTTTTAAGCC
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTC-AAAGTGGCTTTTAAGCC
EST: gi|5650286|gb|AI920646.1|AI920646
EST:     ATGAGGCTGGAAATGTGAGGACCCGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|148963944|gb|EE015066.2|EE015066
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|37385128|gb|CF629683.1|CF629683
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|45568545|gb|CK986116.1|CK986116
EST:     GTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGC-TTTATGCCA
genomic: GTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|211540749|gb|FL105307.1|FL105307
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|60352524|gb|DN219497.1|DN219497
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|211086351|gb|FL105311.1|FL105311
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|67042195|gb|CO468450.1|CO468450
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|32793479|gb|CD945715.1|CD945715
EST:     ATGAGGCTGCAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTT
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTT
EST: gi|5901142|gb|AW042242.1|AW042242
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
EST: gi|116822041|gb|EC865407.1|EC865407
EST:     ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCGG                         GGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA
genomic: ATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCA

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: 167

GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 391

GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 504

GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcc ... gtgcatgcagGGAGGGATATCAAATGGTGAAATTATTTACTTCAAAGTGGCTTTTAAGCCAACAGCAACTATCGGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAGgtttttatcctaaaatcttattgctctactacattttttgtgatatagttgtatttcgtatgaaattgctgacttattatttttaacttgtatgtgcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA