Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCTAACGCCAACCCCGTTGTCGCCAAGGTCGTCCTTTCCCTCGACCTGCTCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtacccccaatctcctccatccggctggtcccttccccgtgcttcggctatagattctcgaatctgctggagcgagctgatggggaatttttgaaa...

Basic information

species Zea mays
transcript GRMZM2G049091_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G049091_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g43450.1 (Oryza sativa), 5'ss of exon 1
------------------------CGCTAACGCCAACCCCGTTGTCGCCAAGGTCGTCCTTTCCCTCGACCTGCTCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtacccccaatctcctccatccggctggtcccttccccgtgcttcggctatagattctcgaatctgctggagcgagctgatggggaatttttgaaa
                        | | ||| | |||||||| ||||||||||||||||| ||||| ||||| |||||| | || || | | ||         || |   ||||    | || | | | | ||| |   ||     || ||  ||||        |   |||||   | |       ||  ||   |  | | |  | | || ||         
CGTGTCCTCCTCCGACGCCGCCGGCTCCAACCCTAACCCCGTCGTCGCCAAGGTCGTCCTCTCCCTTGACCTCCTCCGCTCCGAGGAGCCCTCCC-------TCCAGgcaagcct---cccccgcccact-ccctctcccttgcggattcgaatggtagtacattct--cttcgagcaaaatgatatgaccctatggccgtggg--ggttggtaa---------
















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|149087889|gb|EE177157.2|EE177157
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211457542|gb|FL334934.1|FL334934
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211003758|gb|FL418077.1|FL418077
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211386029|gb|FL330041.1|FL330041
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGNAGAGCCCACGCTCCAG                         TTCAAGATSGANTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211176906|gb|FL324248.1|FL324248
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|71321698|gb|DR797541.1|DR797541
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211381303|gb|FL357053.1|FL357053
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211250289|gb|FL313174.1|FL313174
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211472635|gb|FL331977.1|FL331977
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|71330940|gb|DR802278.1|DR802278
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211140890|gb|FL328470.1|FL328470
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAG
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAG
EST: gi|211461941|gb|FL313809.1|FL313809
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGA
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGA
EST: gi|4647272|gb|AI622347.1|AI622347
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|149111893|gb|EE191049.2|EE191049
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|148942185|gb|EC887190.2|EC887190
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211306084|gb|FL334837.1|FL334837
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|148999712|gb|EE036711.2|EE036711
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|74242554|gb|DT650468.1|DT650468
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|91869046|gb|EB400256.1|EB400256
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211291843|gb|FL361720.1|FL361720
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATA
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATA
EST: gi|60341247|gb|DN208220.1|DN208220
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211460303|gb|FL343035.1|FL343035
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211228786|gb|FL333948.1|FL333948
EST:     CCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: CCGCCCAGAAGAACGCCCCGAAGAGCGCCCGG-AAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211281507|gb|FL337114.1|FL337114
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211183380|gb|FL324632.1|FL324632
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCC-ACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211133431|gb|FL346182.1|FL346182
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCC-ACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211002531|gb|FL365072.1|FL365072
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211478501|gb|FL368099.1|FL368099
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGARCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211108623|gb|FL325820.1|FL325820
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTYGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211342584|gb|FL343866.1|FL343866
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211233734|gb|FL380048.1|FL380048
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
EST: gi|211234944|gb|FL328591.1|FL328591
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATAC
EST: gi|78083457|gb|DV511850.1|DV511850
EST:     TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAG                         TTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC
genomic: TCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 87

CGCTAACGCCAACCCCGTTGTCGCCAAGGTCGTCCTTTCCCTCGACCTGCTCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 94

CGCTAACGCCAACCCCGTTGTCGCCAAGGTCGTCCTTTCCCTCGACCTGCTCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 123

CGCTAACGCCAACCCCGTTGTCGCCAAGGTCGTCCTTTCCCTCGACCTGCTCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 89

CGCTAACGCCAACCCCGTTGTCGCCAAGGTCGTCCTTTCCCTCGACCTGCTCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtaccc ... acaacgacagTTCAAGATGGAGTTGGCACAAACTAACACTGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTGCCTATGTGTGTTTTCTCCGAAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCTAACGCCAACCCCGTTGTCGCCAAGGTCGTCCTTTCCCTCGACCTGCTCCGCCCAGAAGAACGCCCCGAAGAGCGCCCGGAAGAGCCCACGCTCCAGgcaagtacccccaatctcctccatccggctggtcccttccccgtgcttcggctatagattctcgaatctgctggagcgagctgatggggaatttttgaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttcccc