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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctgtgaaggaaaacagcaagtgctctggaattctagtatgttgacatgtgtcatgtgtgggtttgatgagtgatggatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAGGAAGGGCAGATCTACCTGGCGTCCCCCTACACCGCTGCAGCCTCGGCCC

Basic information

species Zea mays
transcript GRMZM2G370852_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g03260.3 (Oryza sativa), 3'ss of exon 12
--gtctgtg-aaggaaaacagcaagtgctctg-gaattctagtatgttgacatgtgtcatgtgtgggtttgatgagtgatggatctggtaacctggat---gtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAGGAAGGGCAGATCTACCTGGCGTCCCCCTACACCGCTGCAGCCTCGGCCC
   |   || || |  ||  ||||||| |||   |||| ||   ||||||   | ||       || |||| ||| | |  ||| |   || |    |   |||||||| || ||||| || ||||||||||| ||||| |||||||||||||||||||||||||||||||||||||| || || | |||||| || || || ||||
tccttaatgcaaagggaattgcaagtgttctccaaattatatcctgttgatgcgagt-------ggttttgttgattaactgatttcaaaaacgtatttgggtgcagGTGTGTGTGTCGACGACGAACAGGAATTTCCCCGGCAGGATGGGGCACAAGGAAGGGCAGATCTACCTGGCTTCGCCGTTCACCGCGGCGGCTTCAGCCC

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 14
gtctgtgaaggaaaacagcaagtgctctggaattctagtatgttgacatgtgtcatgtgtgggtttga-tgagtgatggatctggtaac---ctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAGGAAGGGCAGATCTACCTGGCGTCCCCCTACACCGCTGCAGCCTCGGCCC
   |||  |             |||| |   || ||  | |    | |||       || | || ||| | | | |      ||   ||   |||| ||||||||| || || || || ||||||||||||||||||||| | ||||| ||||||||||| || |||||  |||| ||||| || || ||||| || || ||  
---tgttcatctgccatatggttgcttttatatgctt-tctacataaatgatgagattgagagtctgagtaatttactccattgcctacgtgctggttgtgcagGTTTGTGTTTCAACTACGAACAGGAACTTCCCGGGCCGAATGGGACACAAGGAAGGTCAAATCTATTTGGCTTCCCCTTATACAGCTGCTGCATCTGCAT

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 14
gtctgtgaaggaaaacagcaagtgctctggaattctagtatgttgacatgtgtcatgtgtgggtttgatgagtgatggatctggtaac---ctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAGGAAGGGCAGATCTACCTGGCGTCCCCCTACACCGCTGCAGCCTCGGCCC
   |||  |             |||| | | || ||       | |    ||  || || |  | |||  | | |      || | ||   |||| ||||||||| || || || || ||||||||||||||||||||| | ||||| ||||||||||| || |||||  |||| ||||| || || ||||| || || ||  
--ttgttcatctgccatatggttgcttttgtatgctttctacataagtgatgagat-tgagaatctgagtatttactccattgtttacacgctggttgtgcagGTTTGTGTTTCAACTACGAACAGGAACTTCCCGGGCCGAATGGGACACAAGGAAGGTCAAATCTATTTGGCTTCCCCATATACAGCTGCTGCATCTGCAT

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 14
gtctgtgaaggaaaacagcaagtgctctggaattcta-gtatgttgacatgtgtcatgtgtgggtttgatgagtgatggatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAGGAAGGGCAGATCTACCTGGCGTCCCCCTACACCGCTGCAGCCTCGGCCC
||  ||       |    |      | |  |||| |  | |  |   |   | |     ||| |  | |  |  || |  | |   ||  |   | | ||||| || || || || || |||||||||||||| ||  ||||||| ||||| |||||||| || ||| | ||||| || ||||| ||||||||||||||  
gtacgtacccattacttaccctacttatccaattatctgcacttcacctattcttgaaagtgagactaacaaa-gacgtgttttaaaatgtttgt-tacagGTGTGTGTCTCAACGACAAACAGGAACTTCCCCGGTCGGATGGGACACAAAGAAGGGCAAATTTACTTAGCGTCTCCTTACACTGCTGCAGCCTCGGCTT

upper sequence: GRMZM2G370852_T02 (Zea mays), 3'ss of exon 13
lower sequence: EDO97224 (Chlamydomonas reinhardtii), 3'ss of exon 11
--gtctgtgaaggaaaacagcaagtgctctggaattctagtatgttgacatgtgtcatgtgtgggtttgatgagtgatggatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAGGAAGGGCAGATCTACCTGGCGTCCCCCTACACCGCTGCAGCCTCGGCCC
  | ||      |     ||    |||     |  |||  |   |   |||    |   ||  |          ||      |     |  |||  |  ||||| |||||||||||||| ||| | |||||||| ||| | ||||| |||||||| || |||||||||||||| || ||||||||||| || ||||| ||||
ccggctcccggcgtccttagtccatgcaaccaatctcttctcactcaccatacccccc-tgccgccgctgccgctggccctccgccgcatgtggccgc-cagGTGTGCGTGTCCACCACCAACCGCAACTTCCCCGGCCGCATGGGCCACAAGGAGGGCCAGATCTACCTGGCCTCGCCCTACACCGCCGCCGCCTCCGCCC

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|149051576|gb|EE155676.2|EE155676
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|37375881|gb|CF624420.1|CF624420
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|76282892|gb|DV022460.1|DV022460
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|24765664|gb|CA400823.1|CA400823
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|211032048|gb|FL269121.1|FL269121
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|16927655|gb|BM080724.1|BM080724
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|71771493|gb|DR969430.1|DR969430
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGGACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|76924561|gb|DV170009.1|DV170009
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTTTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|101395254|gb|EB819557.1|EB819557
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|16916456|gb|BM072849.1|BM072849
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|110532595|gb|EE036775.1|EE036775
EST:     CTTGTCTGGGGGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|31350830|gb|CD435187.1|CD435187
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|60341015|gb|DN207988.1|DN207988
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|74238621|gb|DT646535.1|DT646535
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|78076215|gb|DV504649.1|DV504649
EST:     CTTGTTTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTTTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|211090106|gb|FL396339.1|FL396339
EST:     CYTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTC
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTC
EST: gi|71445105|gb|DR826155.1|DR826155
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|71763036|gb|DR960973.1|DR960973
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|211011802|gb|FL408548.1|FL408548
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|149080159|gb|EE169177.2|EE169177
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|211350370|gb|FL368852.1|FL368852
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAAACAG-AACTTCCCGGGCAGGATGGGGCACAA
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAA-CAGGAACTTCCCGGGCAGGATGGGGCACAA
EST: gi|148971978|gb|EE022780.2|EE022780
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|74246484|gb|DT654398.1|DT654398
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|149079940|gb|EE168953.2|EE168953
EST:     CTTGTTTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTTTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|37418663|gb|CF647003.1|CF647003
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
EST: gi|110195844|gb|EC877741.1|EC877741
EST:     CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACG                         GTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG
genomic: CTTGTCTGGGTGGCCCTCGCGATACGTATGCACGGATGAATGAACCTACGgtgggtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtgtcatgtgtgggtttgatgagtgatggatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAGGAAGGGCAGATCTACCTGGCGTCCCCCTACACCGCTGCAGCCTCGGCCC
                                    tggtaac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtgaaggaaaacagcaagtgctctggaattctagtatgttgacatgtgtcatgtgtgggtttgatgagtgatggatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTCCCGGGCAGGATGGGGCACAAGGAAGGGCAGATCTACCTGGCGTCCCCCTACACCGCTGCAGCCTCGGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG