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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgtatgttctcgaatatgagctcgtcagcgagacagcgacgacaagaagagctatgattattggagggagctatggttatttaaatccttctttttgtcgtggattatcatctgcaatattcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTGGGCCACCATACCATGAGGAGTGTCAGTGATCATGGTGACACCAAGGAGC

Basic information

species Zea mays
transcript GRMZM2G152477_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152477_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g13540.1 (Oryza sativa), 3'ss of exon 4
gtgcgtgtatgttctcgaatatgagctcgtcagcgagacagcgacgacaagaagagctatgattattggagggagctatggttatttaaatccttctttttgtcgtggattatcatctgcaatattcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTGGGCCACCATACCATGAGGAGTGTCAGTGATCATGGTGACACCAAGGAGC
      ||  |   | | | |||     |||| | |  |         || || ||||||   ||       |||| |   || ||| |||  ||  |||| | | ||  ||  ||||              ||||| |||| | ||| ||||||| ||| || |||  ||||||| |||| || || || |||||||| ||||| |||||||| |||||||||||||||||||
------gtgcgcatttgga-atggaacagtcatcaatgcttaagaacaaaaaaaagctattcctaggttgctgagcaa-aattgttttaatattttattttatgg-ggtctactatct--------------agGATATGGATGAGGCAATGAAGAAATCAACAGCGAAGTGGAAGATTGCTGTTGGGCATCATACCATTAGGAGCGTCAGTGACCATGGTGACACCAAGGAGC
















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|148966045|gb|EE016979.2|EE016979
EST:     GGGAAAACTACATAAACAATCTGCTCAAG                         GATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
genomic: GGGAAAACTACATAAACAATCTGCTCAAGgtgcgtgtat ... ttcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
EST: gi|32845008|gb|CD984689.1|CD984689
EST:     ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAG                         GATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
genomic: ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAGgtgcgtgtat ... ttcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
EST: gi|37426126|gb|CF650813.1|CF650813
EST:     ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAG                         GATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
genomic: ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAGgtgcgtgtat ... ttcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
EST: gi|32845140|gb|CD984821.1|CD984821
EST:     ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAG                         GATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
genomic: ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAGgtgcgtgtat ... ttcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
EST: gi|32844554|gb|CD984235.1|CD984235
EST:     ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAG                         GATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
genomic: ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAGgtgcgtgtat ... ttcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
EST: gi|78114010|gb|DV532399.1|DV532399
EST:     ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAG                         GATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
genomic: ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAGgtgcgtgtat ... ttcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
EST: gi|32844045|gb|CD983726.1|CD983726
EST:     ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAG                         GATTTGGACGGGGTCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
genomic: ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAGgtgcgtgtat ... ttcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
EST: gi|37393857|gb|CF634195.1|CF634195
EST:     ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAG                         GATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
genomic: ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAGgtgcgtgtat ... ttcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
EST: gi|76012839|gb|DT940009.1|DT940009
EST:     AGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAG                         GATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
genomic: AGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAGgtgcgtgtat ... ttcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
EST: gi|32835913|gb|CD975591.1|CD975591
EST:     ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAG                         GATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
genomic: ACTGGAGAGGGGTGGCGCCTCGGGAAAACTACATAAACAATCTGCTCAAGgtgcgtgtat ... ttcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
EST: gi|18162089|gb|BM331928.1|BM331928
EST:     CTGGAGAGGGGTGGCGCGCTCGGGAAAACTACATAAACAATCTGCTCAAG                         GATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG
genomic: CTGGAGAGGGGTGGCGC-CTCGGGAAAACTACATAAACAATCTGCTCAAGgtgcgtgtat ... ttcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttatttaaatccttctttttgtcgtggattatcatctgcaatattcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTGGGCCACCATACCATGAGGAGTGTCAGTGATCATGGTGACACCAAGGAGC
                                         aatattcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgtatgttctcgaatatgagctcgtcagcgagacagcgacgacaagaagagctatgattattggagggagctatggttatttaaatccttctttttgtcgtggattatcatctgcaatattcaattcagGATTTGGACGGGGCCATGAAGACATCGACTGCGGCGTGGAAGGTTGCCGTGGGCCACCATACCATGAGGAGTGTCAGTGATCATGGTGACACCAAGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG