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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtcaggagacaagttttatttcgtttctgtagctggttggaaacaactgtagtaatgtgtatcaatacttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG

Basic information

species Zea mays
transcript GRMZM2G171469_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171469_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g02850.1 (Oryza sativa), 3'ss of exon 3
gtttgtgtcaggagacaagttttatttc--------gtttctgtagctggtt------ggaaacaactgtagtaatgtgtatcaatacttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG
|||||||   ||| |||  || | ||||        ||||||| |  |  ||      |   | |   | | | ||| ||| | |||   | || ||| || ||||||| ||||| |||||||| ||||| || || |||||||| ||||| |||||| ||||||||||||||||||||||||||||||||
gtttgtgggggga-acagtttatgtttctctgacttgtttctgcaatttttttcgaaggtgcaaagtaggaatgatgcgtaaccatatggcattgtagGTATTTCAACATGTGCTCATTGATTTTCCGGGGCTTGCATTCTTCACAACCTATGCTCTGTTAGTGCTCTTCTGGGCTGAGATTTACTATCAG

upper sequence: GRMZM2G171469_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 3
gtttgtgtcaggagac-aagttttatttcgtttctgtagctggttggaaacaactgtagtaatgtgtatcaatacttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG
      || |||| |  |||| || |   |||||| ||   | |            |  |  | | | || |    |   | |||||  | |||    | ||| | ||||| || || ||   |||||||||||| ||  || ||||||| ||||||||||||||||||||  | |||
------gtgaggaaatgaagtcttttggagtttctctaaacgatc-----------tcttcctttttctctactgctttatgtagATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACGTATACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAG

upper sequence: GRMZM2G171469_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ23006 (Selaginella moellendorffii), 3'ss of exon 3
gtttgtgtcaggagacaagttttatttcgtttctgtagctggttggaaacaactgtagtaatgtgtatcaatacttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG
           | ||  | ||  | |    || || || |  |   ||  | || |  |  | | | || |    |   | |||||  | |||    | ||| | ||||| || || ||   |||||||||||| ||| || ||||||| ||||||||||||||||||||  | |||
-----------gtgaggaattgaagtc---ttttggagtttctctaaacgatctct--tcctttttctctactgctttatgtagATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAG

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|211394911|gb|FL373461.1|FL373461
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|211280348|gb|FL373309.1|FL373309
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|211494351|gb|FL425169.1|FL425169
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|78108686|gb|DV527104.1|DV527104
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|32870547|gb|CF010229.1|CF010229
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACATGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|211249778|gb|FL400508.1|FL400508
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGSCGGGCCTAGCGTTCTTCAAGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|149017006|gb|EE045660.2|EE045660
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|211330706|gb|FL425856.1|FL425856
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|91873273|gb|EB403230.1|EB403230
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|78108178|gb|DV526596.1|DV526596
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|71322323|gb|DR797838.1|DR797838
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|211015090|gb|FL429494.1|FL429494
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACATGTGCTTATTGATTTG
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTG
EST: gi|211278771|gb|FL390080.1|FL390080
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCAC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCAC
EST: gi|50339374|gb|CO534500.1|CO534500
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|76018861|gb|DT946031.1|DT946031
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|5895618|gb|AW036864.1|AW036864
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|74237785|gb|DT645699.1|DT645699
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|211503826|gb|FL372211.1|FL372211
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|211060391|gb|FL405187.1|FL405187
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCT
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCT
EST: gi|211461108|gb|FL380552.1|FL380552
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|50333507|gb|CO528633.1|CO528633
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|71770532|gb|DR968469.1|DR968469
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|149075806|gb|EE164341.2|EE164341
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACC
EST: gi|211504995|gb|FL428970.1|FL428970
EST:     GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAG                         ATACTTCAACACGTGCTTATTGATTT
genomic: GGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 152

TGAGGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 160

TGAGGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 153

TGAGGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 238

TGAGGTCAACCGAGTTTGTACTGCGGCGGGATGTGCAACTTGTACACCCTGAGgtttgtgtca ... ttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgtagctggttggaaacaactgtagtaatgtgtatcaatacttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG
                                          tacttcctttt  CT-rich tract
                                    tatcaata  TA-rich tract