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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaacttctagagctcattctttttccaacatattgagagaaaagtaatgtagatagttttgtttcttatgaaaaaacatgcatatcctgactgcgatatttctgctaaaccttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGGTTGTCT

Basic information

species Zea mays
transcript GRMZM2G091503_T04
intron # 4
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 4
lower sequence: LOC_Os08g41250.2 (Oryza sativa), 3'ss of exon 3
gtatgcaaacttct-agagctcattctttttccaacatattgaga-gaaaagtaatgtagatagttttgtttcttatgaaaaaacatgcatatcctgactgcgatatttctgctaaaccttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGGTTGTCT
||| |  ||||||| ||||   | | ||||   ||||| |||| | |||| | || | |||   |  ||||    ||  | || ||||||| | |||||| | |||| | || |  |  ||| ||||      | ||||||| || ||||||||||||||| ||| || |||| |||||||||||||| ||||||||||||||||||||||||||||||||| |||| ||||   | || |
gtaaggcaacttcttagagacaaatatttta--aacatcttgatatgaaatgaaaggaagactatcctgtt----atatagaaccatgcatttgctgactacaatatat-tgatgcatgttcttgtt----cgctctgcagAGAGGCAAAGTAAAACCTGTTCATGTTGTTGACGTTCCTGGTCATGCAAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTCAAGCAGCTGGAATAGTTT

upper sequence: GRMZM2G091503_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 2
gtatgcaaacttctagagctcattctttttccaacatattgagagaaaagtaatgtagatagttttgtttcttatgaaaaaacatgcatatcctgactgcgatatttctgctaaacc-------ttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGGTTGTCT-------------------------------------------------
             ||   |   |  ||      | |||||   ||  ||   |   |||   | | |||    ||| | ||||||| || | ||||||    |     ||   |          |  ||||| |  ||| |||||||||  |||| |||| ||||| ||| || |||||||||||||||||||  ||||||||||||| |||||||||||||||||| |||| |||| | | || |                                                 
------------gtaagacgactcattacagagaaatattttcagcgaaagga---agactatctggtt----atgtagaaacatgtatttgctgactaaagtgcaattgaacagatggcttgatctctgttcttgttctctgcagaaaagcaaaataaagcctgttcatgttgttgatgttcctggtcatgcagGGCTCAAACCCAAGCTTGATGAAGTCCTGCCTCAAGCAGCTGGGATAGTTTTTGCTGTTGATGCTCAAGATTTCTTGTCCACCATGCAAGTCGTTGCAGA
















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:     CA-TGGAAGAAA-CAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTACAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|211020826|gb|FL435096.1|FL435096
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|78544806|gb|DV622304.1|DV622304
EST:     TTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: TTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|60399201|gb|DN232015.1|DN232015
EST:     AAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: AAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|211433350|gb|FL131195.1|FL131195
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|26557413|gb|CA829648.1|CA829648
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|60339827|gb|DN206800.1|DN206800
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|60346742|gb|DN213715.1|DN213715
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|211513168|gb|FL138424.1|FL138424
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACATGTGCATATTATTGATGTT
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTT
EST: gi|26456106|gb|CA827689.1|CA827689
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|211515523|gb|FL138439.1|FL138439
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTTGATGTT
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATT-GATGTT
EST: gi|21809710|gb|BQ668028.1|BQ668028
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|89106845|gb|DY577062.1|DY577062
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|22935960|gb|BU572235.1|BU572235
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|60344808|gb|DN211781.1|DN211781
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|211513175|gb|FL138431.1|FL138431
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACATGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|22818765|gb|BU498855.1|BU498855
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|26559708|gb|CA831943.1|CA831943
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|22520628|gb|BU079439.1|BU079439
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|32914426|gb|CF019238.1|CF019238
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|26559949|gb|CA832184.1|CA832184
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG
EST: gi|211515519|gb|FL138435.1|FL138435
EST:     CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGG                         AAAGACAAAGTAAAAC-TGTGCATATTATTGATGTTCCTGGTCATGCTAGG
genomic: CAATGGAAGAAAACAGTGATACTTTTGTGCTGCATTCGGAGCAAGAAAGGgtatgcaaac ... ttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatatcctgactgcgatatttctgctaaaccttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGGTTGTCT
                        tgctaaa  putative branch site (score: 2)
                               ccttcctgttgtcctt  CT-rich tract
                 atatttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaaacttctagagctcattctttttccaacatattgagagaaaagtaatgtagatagttttgtttcttatgaaaaaacatgcatatcctgactgcgatatttctgctaaaccttcctgttgtccttccctgcagAAAGACAAAGTAAAACCTGTGCATATTATTGATGTTCCTGGTCATGCTAGGCTCAAACCCAAACTTGATGAAGTCCTGCCTAAAGCTGCTGCGGTTGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC