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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggccattcttactgtcgatcagaacttacatttgacaaactaattaaactgtcgatcaggtagcaccatggctgcatcagcgtcactgaaaaacaaacaaaaaactgaaataatcgcctcgatcttctttctagTTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGGCCGCTGGGCATGGAGCTGTTCCAGAAGGAACAAGATGACTTGCTCTCGGACCTGAACGAC

Basic information

species Zea mays
transcript GRMZM2G065012_T03
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065012_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 13
gtatggccattcttactgtcgatcagaacttacatttgacaaactaattaaactgtcgatcaggtagcaccatggctgcatcagcgtcactgaaaaacaaacaaaaaactgaaataatcgcctcgatcttctttctagTTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGGCCGCTGGGCATGGAGCTGTTCCAGAAGGAACAAGATGACTTGCTCTCGGACCTGAACGAC
|||||     | | |   ||      | |||    || ||| |      ||    |||||||    |    |||| |     |   ||||      |||| |  |  ||||| |    |   |  |  |   |   |||||||| ||||||||||| || ||||||||||  |||||||| ||||| |  || |||||  |||| |||||||| ||| ||||||| |||||||| |||
gtatga----tgtcatcttccccagaagcttcaccttcacatatgg--caatgcatcgatcaatctg----atggttttgcaaagatcac------acaaccttaccactgacaattccaaattaacatg--tgacagTTCATTTAACGACAAGCCCATTAGGGAGACAGTAGCTGGGCCACTGGGTAAAGAACTGTTTGAGAAAGAACAAGAAGACCTGCTCTCCGACCTGAATGAC
















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|149102174|gb|EE287594.2|EE287594
EST:     TCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGG                         TTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGGCCGCTGGGCAT
genomic: TCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGGgtatggccat ... ttctttctagTTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGGCCGCTGGGCAT
EST: gi|50323441|gb|CO518567.1|CO518567
EST:     TCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGG                         TTCATTCAACGACAAGCCGATCA
genomic: TCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGGgtatggccat ... ttctttctagTTCATTCAACGACAAGCCGATCA
EST: gi|22545340|gb|BU097699.1|BU097699
EST:     TCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGG                         TTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGGCCGCTGGGCAT
genomic: TCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGGgtatggccat ... ttctttctagTTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGGCCGCTGGGCAT
EST: gi|116827521|gb|EC871429.1|EC871429
EST:     TCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGG                         TTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGGCCGCTGGGCAT
genomic: TCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGGgtatggccat ... ttctttctagTTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGGCCGCTGGGCAT
EST: gi|211180217|gb|FK950408.1|FK950408
EST:     TCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGG                         TTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGGCCGK-GGNCAT
genomic: TCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGGgtatggccat ... ttctttctagTTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGGCCGCTGGGCAT
EST: gi|211180216|gb|FK950407.1|FK950407
EST:     TCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGG                         TTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGG
genomic: TCGCTCGGGAAAGTCCTGAACACACCAGAAGTCATGCGTGTCTACATAGGgtatggccat ... ttctttctagTTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtcactgaaaaacaaacaaaaaactgaaataatcgcctcgatcttctttctagTTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGGCCGCTGGGCATGGAGCTGTTCCAGAAGGAACAAGATGACTTGCTCTCGGACCTGAACGAC
                                     cctcgatcttctttct  CT-rich tract
         aaaaacaaacaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggccattcttactgtcgatcagaacttacatttgacaaactaattaaactgtcgatcaggtagcaccatggctgcatcagcgtcactgaaaaacaaacaaaaaactgaaataatcgcctcgatcttctttctagTTCATTCAACGACAAGCCGATCAGGGAGACAGCGGCTGGGCCGCTGGGCATGGAGCTGTTCCAGAAGGAACAAGATGACTTGCTCTCGGACCTGAACGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG