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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAACAGCAGGTTAGCCTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctcttatacttgattggctatttgtaccccctaaatgtctcatacttacctttgtgttatctgaacatttgtcagacacattagaataaggct...

Basic information

species Zea mays
transcript GRMZM2G004459_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G004459_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g59590.1 (Oryza sativa), 5'ss of exon 3
CGAACAGCAGGTTAGCCTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctcttatacttgattggctatttgtaccccctaaatgtc--tcatacttacctttgtgttatctgaacatttgtcagacacattagaataaggct
||| |||||||| |||||||| ||||| |||||||||||||||||| | ||| | ||||| ||||| |||||||||||||| || ||||| |||||||||||       | |  |||  || |    ||  |     | |  |||   |||  || |  |  |  |  ||  || | | | |  |      |   |   | |
CGAGCAGCAGGTCAGCCTTGAGCAGGTGATGGCGCCCATCATGCAGACATTCAGAGAGATCGAGACCTGCATTGAGTGCTCTGCGCTTCGCCAGATCCAGgttaaatg-cgtgcactcaatagttctttgttgattacaacttgttggtcaatctgaattgggcatgctcaaaatactagcccaat-tgccatccttttgtt

upper sequence: GRMZM2G004459_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g62570.1 (Oryza sativa), 5'ss of exon 3
CGAACAGCAGGTTAGCCTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctcttata--cttgattggctatttgta---ccccctaaatgtctcatacttacctttgtgttatctgaacatttgtcagacacattagaataaggct
 ||  ||||||  |  |||||    || ||||| |||||||||    | ||||| ||||| ||||| |||||||||||||| || ||||| ||||||| |||         |  |  | | |||   | ||  ||     | || |       || |||  |    ||    ||| ||||   | ||  | ||    | ||  ||
TGAGGAGCAGGGAACTCTTGATGCCGTGATGGCACCCATCATGGTTGCATTCCGAGAGATCGAGACCTGCATTGAGTGCTCTGCGCTTCGCCAGATCCTGgttaatatgtctgcagtcataattttgtgttgataggttgctctgagatagggatgcttggcacattg----ctgcacataattaagtta-atagctacaacact

upper sequence: GRMZM2G004459_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G37730.1 (Glycine max), 5'ss of exon 3
CGAACAGCAGGTTAGCCTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctcttatacttgatt------ggctatttgtaccccctaaatgtctcatacttacctttgtgttat---ctgaacatttgtcagacacattagaataaggct------------
  | |||||||| ||||| |||||||||||| | || || |||||    |||||||||||||| || ||||||||||| || ||   | |||| || |||||  |   | |  ||   | |         ||| ||||     |    | | | | |  | |   |   ||||    |||   | | | | |||  ||   || |   |            
GAATCAGCAGGTGAGCCTAGAACAGGTTATGTCACCAATTATGCAACAGTTCCGCGAGATTGAAACTTGCATTGAGTGTTCAGCATCTAGGCATATTCAGgtatcttttgtactaaccgttgctatcaaactacttgttttgacatcttattttaaagcttctggtcaattatattttgattttgttttatacaatttgctattatattttcttgttgaag

upper sequence: GRMZM2G004459_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ05317 (Selaginella moellendorffii), 5'ss of exon 3
CGAACAGCAGGTTAGC-CTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtccccc-ctcttatacttgattggctatttgtaccccctaaatgtctcatacttacctttgtgttatctgaacatttgtcagacacattagaataaggct
 | |||    |  |   || || || || ||||| || ||||||||   ||| |||||||||||||||||||| |||||||| ||  |    |  || |||||      || || | ||||  |||||         | ||    |||| | ||  |  | || |                                     
-GGACAAGGAGCCAATGCTGGAGCAAGTCATGGCTCCTATCATGCACGACTTTCGCGAGATTGAGACATGCATCGAGTGCTCGGCGTTGAAACGAATACAGgtatgaagcttttcttcttg--tggct---------cactgggagtctaaaacccatttatgagcag----------------------------------

upper sequence: GRMZM2G004459_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ25633 (Selaginella moellendorffii), 5'ss of exon 3
CGAACAGCAGGTTAGC-CTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtccccc-ctcttatacttgattggctatttgtaccccctaaatgtctcatacttacctttgtgttatctgaacatttgtcagacacattagaataaggct
 | |||    |  |   || || || || ||||| || ||||||||   ||| |||||||||||||||||||| |||||||| ||  |    |  || |||||      || || | ||||  ||||||||| | | | ||    |||| | ||  |  | || |                                     
-GGACAAGGAGCCAATGCTGGAGCAAGTCATGGCTCCTATCATGCACGACTTTCGCGAGATTGAGACATGCATCGAGTGCTCGGCGTTGAAACGAATACAGgtatgaagcttttcttcttg--tggctattttttctcactgggagtctaaaacccatttatgagcag----------------------------------

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|31361614|gb|CD445971.1|CD445971
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|78084949|gb|DV513342.1|DV513342
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|211289495|gb|FL459844.1|FL459844
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|211153232|gb|FL160597.1|FL160597
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|211289494|gb|FL459843.1|FL459843
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|91053299|gb|EB163717.1|EB163717
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|60339673|gb|DN206646.1|DN206646
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|211153243|gb|FL160608.1|FL160608
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|60340644|gb|DN207617.1|DN207617
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|60354705|gb|DN221678.1|DN221678
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
EST: gi|31358133|gb|CD442490.1|CD442490
EST:     TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAG                         GTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT
genomic: TCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctc ... tttttggcagGTGCCTGAGGTCTTCTATTATGCCCAGAAGGCAGTACTTCACCCAACTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAACAGCAGGTTAGCCTTGAACAGGTTATGGCGCCCATCATGCAGTCCTTCCGCGAGATTGAGACATGCATTGAGTGCTCCGCTCTTCGGCAGATCCAGgtcccccctcttatacttgattggctatttgtaccccctaaatgtctcatacttacctttgtgttatctgaacatttgtcagacacattagaataaggct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT