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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgctgactgcgccaccgccaccgcccccacctcttgggtggcctttctttcttcctttctcgtaccctgctcgatttcgcctcgcccaaccccgacaaaagggagggggaaaagcggaggagtatctgacttttgccaccaatggcgtgtttttttacaacgagatggcgttgttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATG

Basic information

species Zea mays
transcript GRMZM2G113640_T05
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113640_T06 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g06730.1 (Oryza sativa), 3'ss of exon 1
gtactgctgactgcgccaccgccaccgcccccacctcttgggtggcctttctttcttcctttctcgtaccctgctcgatttcgcctcgcccaaccccgacaaaagggagggggaaaagcggaggagtatctgacttttgccaccaatggcgtgtttttttacaacgagatggcgttgttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATG
                                         ||    || |   |  ||   | |  ||  ||| ||   ||   ||  || |  |  |     |      |     ||||     | |||||| ||| |  ||   | ||    |  |      |       || | |||||| || ||||||||||||||||||| |||||||||||||||||||||||||||||||||| |
-----------------------------------------gtaaatttaccgccg-ccgcgcactcactttgc-cggcgtcttgtcttccgattcgcatcgccgcccaaagtggtggcgggaatatgtctgaccttttctgccgccgccgccggtggtggtggtg-------gtcggtgggtgcagGTGGAGCTGGAGCAGTATGCAACGGGCCCTCACATCGCGTCGCGGATGCTCTACACG
















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|211270646|gb|FL248436.1|FL248436
EST:     AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAG                         CTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
genomic: AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAGgtactgctga ... ttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
EST: gi|211270650|gb|FL248440.1|FL248440
EST:     AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAG                         CTGGAGCTGGAGCAGTATGC
genomic: AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAGgtactgctga ... ttgggtgtagCTGGAGCTGGAGCAGTATGC
EST: gi|211270652|gb|FL248442.1|FL248442
EST:     AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAG                         CTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
genomic: AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAGgtactgctga ... ttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
EST: gi|211270657|gb|FL248447.1|FL248447
EST:     AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAG                         CTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
genomic: AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAGgtactgctga ... ttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
EST: gi|211270648|gb|FL248438.1|FL248438
EST:     AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAG                         CTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
genomic: AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAGgtactgctga ... ttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
EST: gi|211270651|gb|FL248441.1|FL248441
EST:     AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAG                         CTGGAGCTGGAGCAGTATGCR-CGGGGCCCTCACATCGCGTCGCGGATGCT
genomic: AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAGgtactgctga ... ttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGG-CCCTCACATCGCGTCGCGGATGCT
EST: gi|211270649|gb|FL248439.1|FL248439
EST:     AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAG                         CTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
genomic: AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAGgtactgctga ... ttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
EST: gi|211270647|gb|FL248437.1|FL248437
EST:     AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAG                         CTGGAGCTGGAGCAGTAT
genomic: AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAGgtactgctga ... ttgggtgtagCTGGAGCTGGAGCAGTAT
EST: gi|211270655|gb|FL248445.1|FL248445
EST:     AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAG                         CTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
genomic: AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAGgtactgctga ... ttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
EST: gi|211270656|gb|FL248446.1|FL248446
EST:     AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAG                         CTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
genomic: AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAGgtactgctga ... ttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
EST: gi|211050250|gb|FL241531.1|FL241531
EST:     AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAG                         CTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC
genomic: AGCAGCTGGAGGGCCTCTTGGGTGGCCTGACCCAGTTCTCCGACCCCAAGgtactgctga ... ttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttgccaccaatggcgtgtttttttacaacgagatggcgttgttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATG
 atctgac  putative branch site (score: 3)
                     tttttttacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgctgactgcgccaccgccaccgcccccacctcttgggtggcctttctttcttcctttctcgtaccctgctcgatttcgcctcgcccaaccccgacaaaagggagggggaaaagcggaggagtatctgacttttgccaccaatggcgtgtttttttacaacgagatggcgttgttgggtgtagCTGGAGCTGGAGCAGTATGCGACGGGCCCTCACATCGCGTCGCGGATGCTCTACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG