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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaacaaggcatatttcttgtctccttttctctttaccttctaatctgattaaacattggcatccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG

Basic information

species Zea mays
transcript GRMZM2G104166_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104166_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g45670.1 (Oryza sativa), 3'ss of exon 2
gtatgaacaaggcatatttctt---------gtctc-cttttctctttaccttc-taatctgattaaacattggcatcctt--gctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG
|||||| |||| || |||| ||         || || |||| || | |||||   | || |   |||||||||||||| ||  || |||||||||||||||||||||| ||||| |||||||| || |||||||| |||||||||||||| || ||||
gtatgagcaagacaaatttattagagaaacagtatctctttcctttctacctagattattttgataaacattggcatcttttggccagCATTTTCAAAGGGACATTGTCCGGGGTGTGGAGGGATACATAGTCACTGGATCTAAACAAGTTGACATAG
















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|93012221|gb|EB637741.1|EB637741
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|91056507|gb|EB166925.1|EB166925
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|50336720|gb|CO531846.1|CO531846
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|148970807|gb|EE021570.2|EE021570
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|91873694|gb|EB403651.1|EB403651
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|211195883|gb|FL115001.1|FL115001
EST:     AACTGCATCAGAGATTGGAAAAACTTTATTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|211195880|gb|FL114998.1|FL114998
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|211304267|gb|FL115004.1|FL115004
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|148996413|gb|EE035708.2|EE035708
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTG-----                         C----T-AAA-GGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|211195879|gb|FL114997.1|FL114997
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|211304269|gb|FL115006.1|FL115006
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|74236878|gb|DT644792.1|DT644792
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|211195882|gb|FL115000.1|FL115000
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTTCGGGGCGTGGAGGGCTATATAGTCACAGG
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTT-CGGGGCGTGGAGGGCTATATAGTCACAGG
EST: gi|211195881|gb|FL114999.1|FL114999
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|76283090|gb|DV022658.1|DV022658
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|26456480|gb|CA828063.1|CA828063
EST:     CTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: CTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|76927135|gb|DV171161.1|DV171161
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|211304266|gb|FL115003.1|FL115003
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|37424980|gb|CF650224.1|CF650224
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|148981761|gb|EE027867.2|EE027867
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|211304268|gb|FL115005.1|FL115005
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|33466753|gb|CF243802.1|CF243802
EST:     AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
EST: gi|211195884|gb|FL115002.1|FL115002
EST:     AACTGCATCAGAGATTGGAAAAACTTTATTTATCGACTCGTGCTGCTAAA                         CATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA
genomic: AACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGA

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: 44 (upstream exon), 49 (downstream exon)
Score: 50

GTTTGGCTACGGGAATTCTGATAATGCGTTTACAGATGAGTCAGAGGTTAAACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

GTTTGGCTACGGGAATTCTGATAATGCGTTTACAGATGAGTCAGAGGTTAAACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

GTTTGGCTACGGGAATTCTGATAATGCGTTTACAGATGAGTCAGAGGTTAAACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

GTTTGGCTACGGGAATTCTGATAATGCGTTTACAGATGAGTCAGAGGTTAAACTGCATCAGAGATTGGAAAAGCTTTACTTATCGACTCGTGCTGCTAAAgtatgaacaa ... tccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctccttttctctttaccttctaatctgattaaacattggcatccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG
                                             tccttgct  CT-rich tract
                               attaaacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaacaaggcatatttcttgtctccttttctctttaccttctaatctgattaaacattggcatccttgctagCATTTTCAAAGGGACATTGTTCGGGGCGTGGAGGGCTATATAGTCACAGGATCTAAACAAGTCGAAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG