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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttgtcaggaacccaactatttgtaaagaacaatcatttccctcgaagaatgtccaagttcagactaatataatggtcgctgtacattttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA

Basic information

species Zea mays
transcript GRMZM2G069765_T05
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 10
attttgtcaggaacccaactatttgtaaagaacaatcatttccctcgaagaatgtccaagttcagactaatataatggtcgctgtacattttcaatg-cagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA
                   ||||||| ||      || | |    |    ||| |   |   ||   | |   |||   |  |    ||| |   || |||||||||||||| ||||||||||||||||||||||| ||||||||  | ||||||||||| ||||| |||||||||||||||||| |||||||||||||||
------------------gtatttgttaa---tgttcctgtggtacctgtaattttgcatgccatgttcac-caataaccatttcttattctttttgacagGATGCCATGTCTGTTGCAAGGAACATTTTGAAAAACCCAAAACTTTTACCTGGAGGTGGTGCTACCGAGCTGACTGTATCAGCAGCACTGAAGCAAAAGA

upper sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 7
attttgtcaggaacccaactatttgtaaagaacaatcatttccctcgaagaatgtccaagttcagactaatataatggtcgctgtacattttc--aatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA
                        ||||||     |   || |  |  |||   |     ||    |      | || |  ||| |  |||||  |   |||||||||||||| || |||||||||||  | |||||| |||||||  |||||||||| || ||||| ||| ||||| ||||||||||||||||||| ||||
------------------------gtaaagt---gttgatttctacccagagcttgtggatttgatc------attgctttctgaagtttttcccatgacagGATGCCATGTCTGTAGCAAGGAACATAATAAAAAATTCAAAACTTGTTCCTGGAGGAGGTGCTACTGAGTTGACTATATCAGCAACACTGAAGCAGAAGA

upper sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G28650.2 (Glycine max), 3'ss of exon 10
attttgtcaggaacccaactatttgtaaagaacaatcatttccctcgaagaatgtccaagttcagactaatataatggtcgctgtacattttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA
                              | | |||       || || ||| |   ||||  ||| |   |  |    |       |||||    |||||||||||||| ||||||||||||||| | |||||||| |||||  |||||||||| || ||||||||| |||| || || ||  |  |||| |||||||
---------------------------gtaagctatcgacatgttctaaaaattt---agttttgaccatactgctttctgaaacttgttttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCTAAACTTGTTCCTGGAGGCGGTGCTACAGAGTTGACGGTGTCGGCTGCCTTGAAACAAAAGA

upper sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 10
attttgtcaggaacccaactatttgtaaagaacaatcatttccctcgaagaatgtccaagttcagactaatataatggtcgctgtac--attttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA
                                 |   |||  | | |   || |    ||||| ||  | ||      ||   | ||  ||||||    |||||||||||||| ||||||||||||||| | ||||||||||||||  ||||||||||||| ||||||||| |||| || |||||  |  |||| || ||||
------------------------------gtaagctattggcatggtctaaagatttagttctgatca-tactgctttctgagaacttattttcttgacagGATGCCATGTCTGTTGCAAGGAACATTATAAAAAATCCAAAACTTGTTCCTGGAGGTGGTGCTACAGAGTTGACAGTGTCAGCTGCCTTGAAACAGAAGA

upper sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 10
lower sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 9
attttgtcaggaacccaactatttgtaaagaacaatcatttccctcgaagaatgtccaagttcagactaatataatggtcgctgtacattttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA
                     || ||       | | |     ||    | || ||  | |      |||  | ||   |     ||||| ||  | |||||||||||||| |||||||| |||||| | ||||| ||||| ||  ||||||| || || || |||||||| || || || || ||| | || || ||||
--------------------gttcgttggtgttatttacaaatct----gtatttcttaatcattcataaccttatatgcctgaaacattgtccctacagGATGCCATGTCTGTTGCAAGAAACATTATCAAAAACCCAAAGCTAGTTCCTGGTGGAGGAGCCACAGAGCTAACCGTTTCTGCCACATTAAAACAGAAGA

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|211183836|gb|FL001293.1|FL001293
EST:     GTTGAGAGAAACCTGCAG                         GATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
genomic: GTTGAGAGAAACCTGCAGgtatttcttc ... ttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
EST: gi|60339469|gb|DN206442.1|DN206442
EST:     TGAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAG                         GATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
genomic: TGAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAGgtatttcttc ... ttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
EST: gi|67025927|gb|CO454676.1|CO454676
EST:     TGAGGGGAACCAGCAAGGATGTATTGAATGAAGTTGAAAGAAAC-TGCAG                         GATGCCATGTCCGTTGCCAGGA-CATTTTG
genomic: TGAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAGgtatttcttc ... ttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTG
EST: gi|33093954|gb|CF053948.1|CF053948
EST:     TGAGGGGAGCAAGCAAGGATGTATTGAAT-AAGTTGAGAGAAACCTGCAG                         GATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
genomic: TGAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAGgtatttcttc ... ttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
EST: gi|166509795|gb|EG256589.1|EG256589
EST:     AAGTTGAGAGAAACCTGCAG                         GATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
genomic: AAGTTGAGAGAAACCTGCAGgtatttcttc ... ttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
EST: gi|67013717|gb|CO442466.1|CO442466
EST:     GAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCCTGCAG                         -ATGCCATGTNCGTTGCAAGGA-CATTTTGAAAA
genomic: GAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACC-TGCAGgtatttcttc ... ttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAA
EST: gi|32932271|gb|CF037083.1|CF037083
EST:     TGAGGGGAGCAAGCAGGGATGTATTGAATGAAGTTGAGAGAAACCTGCAG                         GATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
genomic: TGAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAGgtatttcttc ... ttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
EST: gi|32934718|gb|CF039530.1|CF039530
EST:     TGAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAG                         GATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
genomic: TGAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAGgtatttcttc ... ttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
EST: gi|22545904|gb|BU098263.1|BU098263
EST:     TGAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAG                         GATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
genomic: TGAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAGgtatttcttc ... ttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
EST: gi|211183835|gb|FL001292.1|FL001292
EST:     GTTGAGAGAAACCTGCAG                         GATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
genomic: GTTGAGAGAAACCTGCAGgtatttcttc ... ttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
EST: gi|78083039|gb|DV511432.1|DV511432
EST:     CAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAG                         GATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
genomic: CAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAGgtatttcttc ... ttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT
EST: gi|33093289|gb|CF053283.1|CF053283
EST:     TGAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAG                         GATGCCATGTCCGTTGCAAGGAACATTTTGAANAATCCAAAACTCCTTCCT
genomic: TGAGGGGAGCAAGCAAGGATGTATTGAATGAAGTTGAGAGAAACCTGCAGgtatttcttc ... ttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaagaatgtccaagttcagactaatataatggtcgctgtacattttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA
                   gactaat  putative branch site (score: 2)
                                         cattttc  putative PPT
                    actaatataat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttgtcaggaacccaactatttgtaaagaacaatcatttccctcgaagaatgtccaagttcagactaatataatggtcgctgtacattttcaatgcagGATGCCATGTCCGTTGCAAGGAACATTTTGAAAAATCCAAAACTCCTTCCTGGAGGTGGCGCTACAGAGCTGACTGTATCAGCAACACTGAAGCAAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA