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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagaatttctatctaaccataggctcacatgttttcttcttcttgttcctcatcaagagcaggggaaacaaaaaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACGTATGACACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCA

Basic information

species Zea mays
transcript GRMZM2G044629_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044629_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 13
----------------gtcagaatttctatctaaccataggc-tcacatgttttcttcttcttgt--tcctcatcaagagcaggggaaacaaa---aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACGTATGACACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCA
                | |     |  |||   |   |||   |||     | |||| || || |  |  | |  ||      || | ||| |    ||| |||||||  |||||||||||||||| ||||| |||||||| || |  |||||  | ||||| |||||||||||||| ||||| |||||||| || ||||| || |
gttcaacttctcagtcgcctatgctcttataacattctagatgtcatgctgtgtctttttgttatgattttgagaaactcatcggtatacatatctgaaaattcagGTTTTGCGGGAGGAGGAATTTGCGCCTGTAAAGAATGCGAATGGCGCGTCTTATGATACCCCTGATAGCGCAAAGCTGATGCTGCTTCGTCTCCATAGTA
















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|149100895|gb|EE186990.2|EE186990
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|71429564|gb|DR810614.1|DR810614
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|166514172|gb|EG308864.1|EG308864
EST:     CGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: CGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|211094109|gb|FL460556.1|FL460556
EST:     NGTTTATATTCGACGCTTTCACATACTGCCCGTCCACGGCACTTTTGGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: -GTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|166625031|gb|EG168092.1|EG168092
EST:     GTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: GTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|37378055|gb|CF625683.1|CF625683
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|211406602|gb|FL094198.1|FL094198
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|78115802|gb|DV534190.1|DV534190
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|149014876|gb|EE044587.2|EE044587
EST:     AGTTTATATTGGACGCCTTCACATACTCCCCGTCCACGGCACTTTTGGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|94477176|gb|EB706134.1|EB706134
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|211119105|gb|FL479440.1|FL479440
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|91052248|gb|EB162666.1|EB162666
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|24769018|gb|CA404147.1|CA404147
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTTGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|32863501|gb|CF003183.1|CF003183
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|71772484|gb|DR970416.1|DR970416
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|16926697|gb|BM079765.1|BM079765
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
EST: gi|14244148|gb|BG841843.2|BG841843
EST:     AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAG                         GTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG
genomic: AGTTTATATTCGACGCCTTCACATACTCCCCGTCCACGGCACTTTTCGAGgtcagaattt ... aaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgttttcttcttcttgttcctcatcaagagcaggggaaacaaaaaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACGTATGACACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCA
                                      aaacaaaaaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagaatttctatctaaccataggctcacatgttttcttcttcttgttcctcatcaagagcaggggaaacaaaaaaacttcagGTCATGCGGGAGGAGGAATTCGCGCCGGTAAAGAACGCCAGCGGCGCAACGTATGACACCCCTGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT