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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctcacctttctagcaattttatgttttcttggcttcagattatcaccctcagattcataataacttgcag

Basic information

species Zea mays
transcript GRMZM2G044629_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044629_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 5
ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctcacctttctagcaattttatgtttt----cttggcttcagattatcaccctcagattcataataacttgcag
 |||||||||||| || |||||||| |||||||| |||||||||||| ||||| |||| ||||||||||| ||||||||||| || || |||||| |||         |    |  | | ||||     || | |||| ||  | ||||| | |||   ||||||||||||
GTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGATTTTGTGTGTTCAAAAGCTTGCTGCTCAATCAAgtgatagtaatgtcttttaaccacaattttactctcttttttaatttcgtttcacatctttaccctgaaatttgaaataacttgcag

upper sequence: GRMZM2G044629_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA08G09170.2 (Glycine max), 5'ss of exon 6
ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTA---GCGAAAgtaatttctcacctttctagcaattttatgttttcttggcttcagattatcaccctcagattcata-ataacttgcag
|||| ||||||||||| ||||| |||||||| || || |||||||| |||||| |||| |  || |  || ||||||||| |||     || ||||| || |||  | ||| |     ||  ||||   | || | |  |  | |    |  |||  |  ||   ||||||
ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtt-tcatttgtcttg----gttcagtttctctcgcattatttggttagatcctcattagtttatgtattgcag

upper sequence: GRMZM2G044629_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G26240.1 (Glycine max), 5'ss of exon 5
ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTA---GCGAAAgtaatttctcacctttctagcaattttatgttttcttggcttcagattatcaccctcagattcata-ataacttgcag
|||| ||||||||||| ||||| |||||||| || || |||||||| |||||| |||| |  || |  || ||||||||| |||     || ||||| || |||  | ||| |     ||  |||||  | || | |     | ||   |  ||   |  ||   ||||||
ATATTGGACTTCCATCTGGAAAATCACTTTTTCAACTTCAAGCTGAGAGGATTTTGTGTGCACAGAGACTAGCTGCTCAAGCTACAAATGAGAgtaagtt-tcatttgtcttg----gttcagtttttcttgcattattcggttacatcctcatcagtttatgtattgcag

upper sequence: GRMZM2G044629_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 5'ss of exon 5
ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctcacctttctagcaattttatgttttcttggcttcagattatcaccctcagattcataataacttgcag
|||| ||||||||||||||||||||||| || || || ||||||||| | ||| |||| |||||||  || |||||||||||||   |      |        | |  |     ||| | | |  ||   || | ||  |  || |   |||  | || ||||||||
ATATTGGACTTCCATCAGGAAAGTCACTCTTTCAACTTCAAGCTGAACGAATTTTGTGTGTTCAAAGACTTGCTGCTCAATCTACAAATGAGGgtaaggttattctgcattctgtttgtttgtatttcatttgacatgctgcccttattatt--ttattacttgcag

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|149081508|gb|EE170644.2|EE170644
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|149015643|gb|EE045441.2|EE045441
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|40337292|gb|CK371362.1|CK371362
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|149014175|gb|EE043721.2|EE043721
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|148958334|gb|EC904558.2|EC904558
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|71429565|gb|DR810615.1|DR810615
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|148982619|gb|EE028417.2|EE028417
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|211249751|gb|FL285806.1|FL285806
EST:     GCTGAA-GGATTCTGTGCGTTCAAAAGCTGGCTGCTNCA-TCTAGCGAAA                         A
genomic: GCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCT-CAATCTAGCGAAAgtaatttctc ... taacttgcag-
EST: gi|211249751|gb|FL285806.1|FL285806
EST:     GCTGAA-GGATTCTGTGCGTTCAAAAGCTGGCTGCTNCA-TCTAGCGAAA                         A
genomic: GCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCT-CAATCTAGCGAAAgtaatttctc ... taacttgcag-
EST: gi|149090039|gb|EE179333.2|EE179333
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|148956834|gb|EC902742.2|EC902742
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|91052249|gb|EB162667.1|EB162667
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCT
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCT
EST: gi|149014877|gb|EE044588.2|EE044588
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|148943648|gb|EC888712.2|EC888712
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|71757247|gb|DR955184.1|DR955184
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|148990989|gb|EE032426.2|EE032426
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|94477177|gb|EB706135.1|EB706135
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTT
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|31354041|gb|CD438398.1|CD438398
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGATCCACTGGTACATAATGACAAGCCCCTTTA
EST: gi|76282035|gb|DV021603.1|DV021603
EST:     AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAA                         GCCCGAGTAACACTGTGCCGA
genomic: AGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctc ... taacttgcagGCCCGAGTAACACTGTGCCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATCGGACTTCCATCAGGAAAGTCACTTTTCCAGCTCCAAGCTGAAAGGATTCTGTGCGTTCAAAAGCTGGCTGCTCAATCTAGCGAAAgtaatttctcacctttctagcaattttatgttttcttggcttcagattatcaccctcagattcataataacttgcag

- - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT