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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcttgttgaattctttagtttcttcccagcttctgccagatagttttggtggctaatattttcatgatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTGCTATGTCGCCGATATG

Basic information

species Zea mays
transcript GRMZM2G044027_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 9
gtaatgcttgttgaattc--tttagtttcttcccagcttctg-ccagatagttttggtggctaatatt-ttcatgatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTGCTATGTCGCCGATATG---------------------------------
|||||||| | |||| |   || |   |  || ||| || || |||| | ||  ||| |  || | |  | ||| || ||  |||||||| ||||| ||||| ||||||||||||||||| |||||||||||||||||||| || || |||                                 
gtaatgctcgctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATGGTTTGTCACCCCTTTTGAAATGTCATTAATTAA

upper sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 8
gtaatgcttgttgaattc--tttagtttcttcccagcttctg-ccagatagttttggtggctaatatttt-catgatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTGCTATGTCGCCGATATG
|||||||| | |||| |   || |   |  || ||| || || |||| | ||  ||| |  || | |  | ||| || ||  |||||||| ||||| ||||| ||||||||||||||||| |||||||||||||||||||| || || |||
gtaatgctcgctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATG
















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|149097834|gb|EE183762.2|EE183762
EST:     ACATTGACGATGGGCGTGTTGGGTAGCA-CTTCATTGCTCAGGCTGTGCG                         TGGCGGACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTCCTG
genomic: ACATTGACGATGGCCGTGTTGT-TAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|32841175|gb|CD980856.1|CD980856
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|14206834|gb|BG840512.1|BG840512
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|32909997|gb|CF014809.1|CF014809
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|6194647|gb|AW146751.1|AW146751
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTG
EST: gi|32841101|gb|CD980782.1|CD980782
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|7216734|gb|AW562856.1|AW562856
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|211032180|gb|FL277400.1|FL277400
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|32850262|gb|CD989943.1|CD989943
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGGCTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|32850632|gb|CD990313.1|CD990313
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|32850554|gb|CD990235.1|CD990235
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|488218|gb|T18799.1|T18799
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCT
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCT
EST: gi|32866186|gb|CF005868.1|CF005868
EST:     ATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: ATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|32850616|gb|CD990297.1|CD990297
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|148945878|gb|EC891170.2|EC891170
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|32840626|gb|CD980307.1|CD980307
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|32849033|gb|CD988714.1|CD988714
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|67016223|gb|CO444972.1|CO444972
EST:     ACATTGACGATGGGCCGTGT-GAGANCAACTTCATTGCTCAGGCTGTGCT                         TGGCGAACCCCT-ACTGTCCA
genomic: ACATTGACGATGG-CCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCA
EST: gi|67013235|gb|CO441984.1|CO441984
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|213192508|gb|FM182601.1|FM182601
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTG
EST: gi|32165003|gb|CD670321.1|CD670321
EST:     AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         TGGCGAACCCCTTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCT
genomic: AACATTGACGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTT-ACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCT
EST: gi|148951041|gb|EC896695.2|EC896695
EST:     ACATTGACGATGGCCGTGTTGTTAGCAACTTCATTTGCTCAGGCTGTGCG                         TGGCGAACCCCTTTACTGTCCAGAAGCCAGGAACACAGACTAAGAGCTTCT
genomic: ACATTGACGATGGCCGTGTTGTTAGCAACTTCATT-GCTCAGGCTGTGCGgtaatgcttg ... gatcttgtagTGGCGAACCCCTT-ACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcccagcttctgccagatagttttggtggctaatattttcatgatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTGCTATGTCGCCGATATG
                              ggctaat  putative branch site (score: 3)
                                 taatattttcatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcttgttgaattctttagtttcttcccagcttctgccagatagttttggtggctaatattttcatgatcttgtagTGGCGAACCCCTTACTGTCCAGAAGCCAGGAACACAGACTAGGAGCTTCTGCTATGTCGCCGATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT