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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgccctgctataaagtttgtttttttagctggaaaaatatcagactacccattttagttgtcccatttaagttatgacgaaagcggttattagaccgaaccaagaattagttgatctcctgcatatatctcttataatttgtttccaatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGAAAACTTGGCGCTAACCTTGAT

Basic information

species Zea mays
transcript GRMZM2G002687_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 7
gtctgccctgctataaagtttgtttttttagctggaaaaatatca-gactacccattttagttgtc-ccatttaagttatgacgaaagcggttattagaccgaaccaagaattagttgatctcctgcatatatctcttataatttgtttccaatgttt--cagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGAAAACTTGGCGCTAACCTTGAT
        |||| |||   |||| ||||    ||||||| ||     | |    ||||||  ||   ||||| || || ||          | | |  | ||  |       |  | | ||| ||    ||    ||   | ||  ||| | || |||  |||||||| |||||||| ||||||||||||| ||||||||| |||||||||||||||||||| ||||||||||||
-----gtttgctttaagcattgtattttag--tggaaaactactgcaattttatattttacctgaggccattcaaattttggtcttca-attaagtcaagcgtcctgtagccttatggttctgcttttcatgggcctgtcatttattttaccattttttccagGTGAACAAATATGCGTTCTCAGGTGGCCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGAT

upper sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os07g17770.1 (Oryza sativa), 3'ss of exon 5
gtctgccctgctataaagtttgtttttttagctggaaaaat-atcagactacccattttagttgtcccatttaagttatgacgaaagcggttattagaccgaaccaagaattagttgatctcctgcatatatctcttataatttgtttccaatgttt--cagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGAAAACTTGGCGCTAACCTTGAT
                         ||| | |||||| | | |    |  || |  |||||||   |||||||| |||||           | ||                |||||    |  | ||||   ||  || ||  | |||||| | |||  ||||||||||||||||| |||||||||||||||||| |  | |||||||||||  ||||||| ||||| ||||||
------------------------gtttcatctggaatatttactcaatcacacgctttagttcggccatttaaattatggta--------tcttg---------------tagttctattatttcatagg-cttataaaagctatttccattattttccagGTGAATAAATATGCTTTCTCAGGTGGCCAGGACACCGTGGAGCTCCATAGGGAACTTGGTGCTAATCTTGAT
















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|37395551|gb|CF635056.1|CF635056
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|6020814|gb|AW065742.1|AW065742
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|91876014|gb|EB405971.1|EB405971
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|211179082|gb|FL345825.1|FL345825
EST:     TCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: TCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|71765216|gb|DR963153.1|DR963153
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|9953034|gb|BE639617.1|BE639617
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|149010068|gb|EE041875.2|EE041875
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|149108285|gb|EE292625.2|EE292625
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|111192905|gb|EE291041.1|EE291041
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|110520053|gb|EE024360.1|EE024360
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|67030403|gb|CO459152.1|CO459152
EST:     CAAATTCGGCGATATACGTGACAGATAGTTCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|37373821|gb|CF623233.1|CF623233
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|149073833|gb|EE162155.2|EE162155
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTTTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|60354415|gb|DN221388.1|DN221388
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|113701058|gb|EE678562.1|EE678562
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|7844633|gb|AW787855.1|AW787855
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|211181701|gb|FL465356.1|FL465356
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAARGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGTTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|71305907|gb|DR789080.1|DR789080
EST:     CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
genomic: CAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGA
EST: gi|166643865|gb|EG146244.1|EG146244
EST:     AAATTCGGCGATATTACGTGACAGATAGTGCTAAAGAAATAAAGACAAAG                         GTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAA
genomic: AAATTCGGCGATA-TACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAA

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: 49 (upstream exon), 48 (downstream exon)
Score: 135

GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGAAAACTTGGCGCTAACCTTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGAAAACTTGGCGCTAACCTTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGAAAACTTGGCGCTAACCTTGAT


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 149

GGGGAGAACACAAAAATGTCAGCTAGTGACGCAAATTCGGCGATATACGTGACAGATAGTGCTAAAGAAATAAAGACAAAGgtctgccctg ... aatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGAAAACTTGGCGCTAACCTTGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaattagttgatctcctgcatatatctcttataatttgtttccaatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGAAAACTTGGCGCTAACCTTGAT
       agttgat  putative branch site (score: 149)
                     atatatctcttataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgccctgctataaagtttgtttttttagctggaaaaatatcagactacccattttagttgtcccatttaagttatgacgaaagcggttattagaccgaaccaagaattagttgatctcctgcatatatctcttataatttgtttccaatgtttcagGTGAATAAATATGCCTTCTCAGGTGGCCAGGACTCAATAGAGCTCCATAGAAAACTTGGCGCTAACCTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT