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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcatgcttattgctagcctacaaaattattgtgccagtattgttctttgctcaaaacaatgtaaaaaatgttttatccatcttttgtgtttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA

Basic information

species Zea mays
transcript GRMZM2G099754_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g02810.1 (Oryza sativa), 3'ss of exon 2
tatcatgcttattgctagcctacaaa--attattgtgccagtattgttctttgctcaaaacaatgtaaaaaatgttttatccatcttttgtgtttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
| ||  || ||||  || | |  |||   |||   |  || | ||||  ||   | | || |||    |  | ||   |  |||||||||| | | |||||||| |||||||  | ||| |||||| | || ||||||||||| || |||||||| || ||||||||||||||||||||  |||||||||| ||||||||||
tttcgggcatattattaacttggaaatccttaccttttcattcttgtcgttatgttataagaattatcaggaagta--actcatcttttgtttctttgtcagACTGAGGTTAGGTTCCTTGGGCAGCTAAGACATCCAAATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCA

upper sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g02830.2 (Oryza sativa), 3'ss of exon 2
tatcatgcttattgctagcctacaaa---attattgtgccagtattgttctttgctcaaaacaatgtaaaaaatgttttatccatcttttgtgtttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
  ||  || ||||  || | |  |||   ||||   |  || | ||||  ||   | | || |||    || | ||   |  |||||||||| | | |||||||| |||||||  | ||| |||||| | || ||||||||||| || |||||||| || ||||||||||||||||||||  |||||||||| ||||||||||
-ttcgggcatattattaacttggaaattcattaccttttcattcttgtcgttatgttagaagaattatcaagaagta--actcatcttttgtttctttgtcagACTGAGGTTAGGTTCCTTGGGCAGCTAAGACATCCAAATTTAGTCAAGTTGATTGGGTATTGCTGCGAAGATGACCACAGGCTGCTTGTGTACGAGTTCA

upper sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G45200.1 (Glycine max), 3'ss of exon 2
tatcatgcttattgctagcctacaaaattattgtgccagtattgttctttgctcaaaacaatgtaaaaa---atgttttatccatcttttgtgtttatgt----cagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
  | ||| | |||| |      |||||    |     | | |||   || ||  |    ||| | |||    | ||||  |  || || |||||||  ||    ||||| ||||| || |  || |||||| |||||||||| ||| ||||||||||||| || || |||||||||||||| ||  |||||||||| || |||||| 
cgtgatg-tgattgttgagtgtcaaaa----taccttaatgttgaaatt-gcagagcgtaatttgaaaccatacgtttatttaattttgtgtgttttggtggtgcaGACGGAGGTGAATTTTCTAGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGCTGCGAAGATGATCACAGGCTGCTTGTGTATGAGTTC-

upper sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G40650.1 (Glycine max), 3'ss of exon 2
tatcatgcttattgctagcctacaaaattattgtgccagtattgttctttgctcaaaacaatgtaaaaaatgttttatccatcttttgtgtttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
                           || |||      | || ||||||  | ||| | ||        | ||| ||   | |||| |  |  || ||||| ||||| || |  || |||||| |||||||||| ||| ||||||||||||| || || || || |||||||| ||  |||||||||| || |||||||
----------------------gtgcgtttttgccttttttttcttcttt-tttaaacccatacg---tttatttaatttttttttttttgtggtg-cagACGGAGGTGAATTTTCTCGGGCAGCTGAGGCATCCTAATCTGGTGAAGTTGATTGGGTACTGTTGTGAAGATGATCACAGGCTGCTTGTGTATGAGTTCA

upper sequence: GRMZM2G099754_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0056g00150.t01 (Vitis vinifera), 3'ss of exon 2
tatcatgcttattgctagcctacaaaattattgtgccagtattgttctttgctcaaaacaatgtaaaaaatgttttatccatcttttgtgtttatgtc---agACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
                       ||  || |  |   |   |  ||||||| |        ||     | || ||| |  |   |  || |||| |||   |||| ||||| ||||   | |||||| |||||||||| ||| ||||||||||||| || ||||| ||||| || || || ||| ||||||| |||||||| |
---------------------gtaagcttgtgtttttatcttctttctttggt-gggttggtgctttgactgatttttttac--tgggtctttacgtctgtagACGGAGGTGAACTTTTTAGGGCAGCTGAGGCATCCCAATCTGGTGAAGTTGATAGGGTATTGTTGCGAGGACGATCACCGGTTGCTTGTGTACGAGTTTA

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|93011916|gb|EB637436.1|EB637436
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTT                         ACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
EST: gi|211014135|gb|FL278358.1|FL278358
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTT                         ACCGAGGTTAACTGCCTGGGGC
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGCCTGGGGC
EST: gi|78089253|gb|DV517627.1|DV517627
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTT                         ACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
EST: gi|32833257|gb|CD972935.1|CD972935
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTT                         ACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
EST: gi|31353226|gb|CD437583.1|CD437583
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTT                         ACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
EST: gi|6564164|gb|AW231786.1|AW231786
EST:     CAGAGAATGGCTT                         ACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
genomic: CAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
EST: gi|71429168|gb|DR810218.1|DR810218
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAAAGAATGGCTT                         ACCAAGGTTAA
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAA
EST: gi|67032695|gb|CO461444.1|CO461444
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTT                         ACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
EST: gi|6637068|gb|AW261340.1|AW261340
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTT                         ACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
EST: gi|149038592|gb|EE155519.2|EE155519
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTT                         ACCGAGGTTAACTGCCTGGG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGCCTGGG
EST: gi|148970123|gb|EE021063.2|EE021063
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTT                         ACCGAGGTTAACTGC
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGC
EST: gi|148962074|gb|EE012878.2|EE012878
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTT                         ACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
EST: gi|148961265|gb|EE011986.2|EE011986
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTT                         ACCGAGGTTAACTGCCTGGGGC
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGCCTGGGGC
EST: gi|76910588|gb|DV163935.1|DV163935
EST:     CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTT                         ACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG
genomic: CAGTCAAGGTGCTCAACAAAGATGGACATCAAGGGCACAGAGAATGGCTTgtgagtggaa ... tttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgctcaaaacaatgtaaaaaatgttttatccatcttttgtgtttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA
         aaaacaatgtaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcatgcttattgctagcctacaaaattattgtgccagtattgttctttgctcaaaacaatgtaaaaaatgttttatccatcttttgtgtttatgtcagACCGAGGTTAACTGCCTGGGGCAGTTGAGGCATCCAAATTTGGTGAAGTTGATCGGATATTGCTGCGAAGATGACCATCGGCTGCTTGTCTACGAGTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT