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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCAAGCAGGCGTACATGCGCGGCAAGAGGGTGCTCGAGATCAACCCCAGGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtaccttaccttacctgcactttgatttgctcgtaaggggcacacacacgaacccgcatacgtgggaggatgttgattcgtttgttcgtgttgattgcaacgtaaaacaacaacag

Basic information

species Zea mays
transcript GRMZM2G141931_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141931_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 14
GAGCAAGCAGGCGTACATGCGCGGCAAGAGGGTGCTCGAGATCAACCCCAGGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtaccttaccttacctgcactttga----tttgctcgtaaggggcacacacacgaacccgcatacgtgggaggatgttgattcgtttgttcgtgttgattgcaacgtaaaacaacaacag
 |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||||| ||||||||   | ||||   |  |    |     |  ||  ||     ||       |   ||  |||||| | |  |     | |  |   || |||   ||    | | |            
CAGCAAGCAGGCGTACATGCGCGGCAAGAGGGTACTCGAGATCAACCCCAGGCACCCCATCATCAAGGAACTCCGTGACAAGGTCGCCCAGGACAGCGAGgtactgaagcttattagatcgacaaaaacctcactaatatttatcatttctttgcttccaaatacgtcgaaaaaaa--aacttatggttttgtgc-aatcttgatgcag-----------

upper sequence: GRMZM2G141931_T02 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 14
-GAGCAAGCAGGCGTACATGCGCGGCAAGAGGGTGCTCGAGATCAACCCCAGGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtaccttaccttacctgcactttgatttgctcgtaaggggcacacacacgaacccgcatacgtgggaggatgttgattcgtttgttcgtgttgattgcaacgtaaaacaacaacag
  |||||||| || |||||||||||||||||||| || ||| |||| || |||||||| || |||||||||||||| || |  || |   || ||   ||||||| ||  || |  | | || ||   | ||| |        | ||    ||   |  |   |  |   |     | |||  | | | | |                         
CTAGCAAGCAAGCATACATGCGCGGCAAGAGGGTTCTTGAGGTCAATCCTAGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAggtacatt--ctaattttctctgtggcct-ctctt------tcctcaactcaattggggtttatctgttaactcacaatcggctttacttttca-----------------------

upper sequence: GRMZM2G141931_T02 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA14G40320.4 (Glycine max), 5'ss of exon 14
GAGCAAGCAGGCGTACATGCGCGGCAAGAGGGTGCTCGAGATCAACCCCAGGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtaccttaccttacctgcactttgatttgctcgtaaggggcacacacacgaacccgcatacgtgggaggatgttgattcgtttgttcgtgttgattgcaacgtaaaacaacaacag
 |||||||| || |||||||||||||||||||| || |||||||| || |||||||| || |||||||||||||| || |  || |   || ||   |||||||   |   ||  |  | |   |  |  ||  | |   | |   |   ||| |  ||  | |      |||| |  |  |      |  |  || ||                 
TAGCAAGCAAGCATACATGCGCGGCAAGAGGGTTCTTGAGATCAATCCTAGGCACCCTATTATCAAGGAGCTCCGAGAGAGAGTAGTAAAGAACCCTGAGgtac---attctagat-tattagaacattttctgaggcatctctttcctcaactcaaatggg-gtttatctgttaacacaatctgctttact--tttcag----------------

upper sequence: GRMZM2G141931_T02 (Zea mays), 5'ss of exon 14
lower sequence: AT4G24190.1 (Arabidopsis thaliana), 5'ss of exon 14
GAGCAAGCAGGCGTACATGCGCGGCAAGAGGGTGCTCGAGATCAACCCCAGGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtaccttaccttacctgcactttgatttgctcgtaaggggcacacacacgaacccgcatacgtgggaggatgttgattcgtttgttcgtgttgattgcaacgtaaaacaacaacag
 |  ||||| || ||||||||||| ||||| || ||||||||||||||  | ||||| |||||||| || |||   || |   | ||    |||   ||||||    |         | | |  |||   |  |      |  ||   | |      | |      |  ||    | |  | |                                 
TAATAAGCAAGCTTACATGCGCGGAAAGAGAGTCCTCGAGATCAACCCACGACACCCTATCATCAAAGAACTCAAGGATAGAATTGCAAGTGACCCAGAGgtaaaacaaacataagacccatcaattcttttttt---tacttactgtctattagagaaataaactaacataccaaattctctcag------------------------------

upper sequence: GRMZM2G141931_T02 (Zea mays), 5'ss of exon 14
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 14
GAGCAAGCAGGCGTACATGCGCGGCAAGAGGGTGCTCGAGATCAACCCCAGGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtaccttaccttacctgcactttgatttgctcgtaag---gggcacacacacgaacccgcatacgtgggaggatgttgattcgtttgttcgtgttgattgcaacgtaaaacaacaacag
 |||||||| || || ||||| |||||||||||||| ||||| ||||| ||||| || |||||||||||||| |  || |  || |   ||||||  ||||||  ||       ||    | | |||| ||     |     |||        |||| |  || || |||| |||            |   | || ||                     
CAGCAAGCAAGCATATATGCGTGGCAAGAGGGTGCTTGAGATAAACCCAAGGCATCCGATCATCAAGGAGCTTCAGGAAAGAGTAGTAAAGGACAGTGAGgtatgttttagagacttttttgtcatttacttaattgtctatgcatttcttataacctggttatgtaggagcatggcacacttaaaatgtatctttatga-------------------

upper sequence: GRMZM2G141931_T02 (Zea mays), 5'ss of exon 14
lower sequence: EFJ17496 (Selaginella moellendorffii), 5'ss of exon 15
GAGCAAGCAGGCGTACATGCGCGGCAAGAGGGTGCTCGAGATCAACCCCAGGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtaccttaccttacctgcactttgatttgctcgtaaggggcacacacacgaacccgcatacgtgggaggatgttgattcgtttgttcgtgttgattgcaacgtaaaacaacaacag
   ||  |||   ||||||||||| ||||| ||||| |||||||| ||| | |||||||||||||||||| | || |  || || | |  | ||| | ||     |   ||    |||| |   |   | || ||||       | ||         | |                                                        
CTCCAGACAGAACTACATGCGCGGAAAGAGAGTGCTGGAGATCAATCCCCGTCACCCCATCATCAAGGAGTTGCGTGGGAAAGTGGAC--GAACAGCCAGAGgt-tcgtctagtttgcattacaa---gatc-taagttctcatctcattgttttctacag-------------------------------------------------------

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|60348795|gb|DN215768.1|DN215768
EST:     GGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAG                         AGCGAGGAGCTGAAGCACACGGCGAGGCT
genomic: GGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtaccttacc ... acaacaacagAGCGAGGAGCTGAAGCACACGGCGAGGCT
EST: gi|67040044|gb|CO466299.1|CO466299
EST:     GGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAG                         AGCGAGGAGCTGAAGCACACGGCGAGGCTGGTGGACCAGACGGCCCTGATG
genomic: GGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtaccttacc ... acaacaacagAGCGAGGAGCTGAAGCACACGGCGAGGCTGGTGTACCAGACGGCCCTGATG
EST: gi|20802334|gb|BQ293384.1|BQ293384
EST:     GGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAG                         AGCGAGGAGCTGAAGCACACGGCGAGGCTGGTGTACCAGACGGCCCTGATG
genomic: GGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtaccttacc ... acaacaacagAGCGAGGAGCTGAAGCACACGGCGAGGCTGGTGTACCAGACGGCCCTGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCAAGCAGGCGTACATGCGCGGCAAGAGGGTGCTCGAGATCAACCCCAGGCACCCCATCATCAAGGAGCTCCGCGACAAGGTCGCCCAGGACAACGAGgtaccttaccttacctgcactttgatttgctcgtaaggggcacacacacgaacccgcatacgtgggaggatgttgattcgtttgttcgtgttgattgcaacgtaaaacaacaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT