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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgatgtgctatcgacaccaatgaatatctcaactcaatctattgttttatgtagtgtttcatgcacatgttttgactaatctttattatttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCGAAGGAG

Basic information

species Zea mays
transcript GRMZM2G111713_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111713_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os07g45300.1 (Oryza sativa), 3'ss of exon 11
----gtgatgtgctatcgacaccaatgaatatctcaactcaatctattgttttatgtagtgtttcatgcacatgttttgactaat-ctttattatttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCGAAGGAG
      ||||   ||  |   |  | ||  |   || |     ||||||| || || |||  |  |||  |||    ||||   | ||| ||| | ||||||||||||||||||||||||||| |||| ||||  || ||||||||||| ||||| || |||
tgaatagatggtttagtggttctgaggagcactgcatc-----ctattgtcttgtgcagtactgtatgttcatcgcatgacagtttcttaattgtatttctgtagAAATTTGAAGCCTATAATACAAAAGGTGAGGTCGTGTCTGGAGATAAGTCAAAAGAG
















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|88758132|gb|DY542273.1|DY542273
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|32845899|gb|CD985580.1|CD985580
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|76923556|gb|DV169545.1|DV169545
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|4827723|gb|AI668415.1|AI668415
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|60340408|gb|DN207381.1|DN207381
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|50337822|gb|CO532948.1|CO532948
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|89251080|gb|DY622866.1|DY622866
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|37383724|gb|CF628889.1|CF628889
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|148938687|gb|EC883023.2|EC883023
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|18181535|gb|BM382745.1|BM382745
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|89248722|gb|DY620508.1|DY620508
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|71420007|gb|DR804974.1|DR804974
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
EST: gi|211237149|gb|FL440871.1|FL440871
EST:     ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAG                         AAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG
genomic: ACCTGGATAAAGCTTTTATACAGCTTACACTTGAGTTTGTTACCAAACAGgtttcgttct ... ttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatgtagtgtttcatgcacatgttttgactaatctttattatttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCGAAGGAG
                             gactaat  putative branch site (score: 2)
                                   tctttattatttttct  CT-rich tract
                      atgttttgactaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgtgctatcgacaccaatgaatatctcaactcaatctattgttttatgtagtgtttcatgcacatgttttgactaatctttattatttttctgtagAAATTTGAAGCCTATAATTCAAAGGGTGCAGTTGTGTCTGGAGACAAGTCGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG