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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attagatcatttggcatttttatcaataccaattcttacaagtaggtgggttatcttgtactatcttttgttgctctcctaattcttttgtgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG

Basic information

species Zea mays
transcript GRMZM2G091503_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091503_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 1
attagatcatttggcatttttatcaataccaattcttacaagtaggtgggttatcttgtactatcttttgttgctctcctaattcttttgtgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG
                                                                            | |||||| |  | | |   | ||||||||||||||| |||||||||||||||||| | |||||||||| |||||| |||||| |||||||| ||||| ||||  || |||
---------------------------------------------------------------------------gtgctaattttgcttttccc-ttagcttcgggatggataatcacatcaaggaactgtgatttcaatggaacaaaacaatgatacgtttgtgcttcattcagAGCTGGAGAGG

upper sequence: GRMZM2G091503_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 2
---attagatcatttggcatttttatcaataccaattcttacaagt--aggtgggttatcttgtactatcttttgttgctctcctaattcttttgtgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG
   ||   | |||    |||    |    | ||  ||| |   | |    || |  |||||| |    ||| | ||  || | ||||||||    | ||    ||||||||||||||||| |||||||||||||||| |||||||||||| ||||||  |||||||| ||||| ||||| ||||  || |||
tgaatcgcaacatcatacatcaccactgttcccttttcatgttaatttgagttgagtatcttttgtc-tctgtggt--ctgtgctaattctccctttctc--tagCTTCGGGATGGATCAACACATCAAGGAACTGTGACTTCAATGGAACAAAACAACGATACTTTCGTGCTTCATTCTGAGCTGGAGAGG

upper sequence: GRMZM2G091503_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv17s0000g08600.t01 (Vitis vinifera), 3'ss of exon 4
---attaga-tcatttggcatttttatcaataccaattcttacaagtaggtgggttatcttgtactatcttttgttgctctcctaattcttttgtgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG
   ||| || ||||| ||    |    | ||     |      || ||  |  ||    || |   || || || |  |    | | |||||  ||  || |||||||| ||||| || ||||||||||||||||||||||| | |||   |||    |  ||||||||||||||  | || |      ||
cctattggaatcattaggagaatccgaccatgtt--tcaaagtaaataaatttgtatatttctttcatgttatgatagttatgtcagtctttcatg--tgccagCTTCGAGATGGTTCTTCACATCAAGGAACTGTTACTTCGACGGATACAAATGAAGCCACTTTTGTGCTGCAAACTGATCCCTTTTGG

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|211515522|gb|FL138438.1|FL138438
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTNCA-TGGAAGAAA-
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTT-CAATGGAAGAAAA
EST: gi|211020826|gb|FL435096.1|FL435096
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|211515518|gb|FL138434.1|FL138434
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGA
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGA
EST: gi|211433350|gb|FL131195.1|FL131195
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|26557413|gb|CA829648.1|CA829648
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|60339827|gb|DN206800.1|DN206800
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|60346742|gb|DN213715.1|DN213715
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|211513168|gb|FL138424.1|FL138424
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAB                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|211513170|gb|FL138426.1|FL138426
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTKGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|26456106|gb|CA827689.1|CA827689
EST:     TAGTTCCATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|211515523|gb|FL138439.1|FL138439
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|21809710|gb|BQ668028.1|BQ668028
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|89106845|gb|DY577062.1|DY577062
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|22935960|gb|BU572235.1|BU572235
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|60344808|gb|DN211781.1|DN211781
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|211513175|gb|FL138431.1|FL138431
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|211515531|gb|FL138440.1|FL138440
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|22818765|gb|BU498855.1|BU498855
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|26559708|gb|CA831943.1|CA831943
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|22520628|gb|BU079439.1|BU079439
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|211513172|gb|FL138428.1|FL138428
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCRAGGAACTGTTACTTCAATGGAAG
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAG
EST: gi|32914426|gb|CF019238.1|CF019238
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|26559949|gb|CA832184.1|CA832184
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
EST: gi|211515519|gb|FL138435.1|FL138435
EST:     TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAG                         CTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC
genomic: TAGTTCTATCTGGGCTTAGTGGCAGTGGCAAAACCACTATTTACTACCAGgtaacttcca ... tgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgggttatcttgtactatcttttgttgctctcctaattcttttgtgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG
                               tcctaat  putative branch site (score: 2)
                                     ttcttttgt  CT-rich tract
                                  taattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attagatcatttggcatttttatcaataccaattcttacaagtaggtgggttatcttgtactatcttttgttgctctcctaattcttttgtgcttgtcagCTTCGGGATGGATCATCACATCAAGGAACTGTTACTTCAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA