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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttctgctcatattattattataattgtcttgtctgtttttactgtattcactaatcttgtttctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG

Basic information

species Zea mays
transcript GRMZM2G105019_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 5
--gtgtgttctgctcatattattattataa-ttgtct-tgtctgtt--tttactgtattcactaatcttgtttctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG
  ||||    |    |||  ||| ||  || |  ||| | | |  |  ||||||||  ||||||||   |  |  |||| ||||| ||||| || |||||||| ||||| || || || |||||||||||||| |||||||||||||||
gtgtgtaccttaacaataa-attgttgcaaatcatctatatttactaatttactgtgctcactaattaagccttccattttagTTAAGTGTGTCGATTGAAGTCCCTGGAGAGGAGCCGTACCATTTTCAGCCTCGTCTGTTTTCTAAG
















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|67041846|gb|CO468101.1|CO468101
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGA-CCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|67031272|gb|CO460021.1|CO460021
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|149074736|gb|EE163165.2|EE163165
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCCATTTTCAGCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACC-ATTTTCAGCC
EST: gi|31358963|gb|CD443320.1|CD443320
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGGTGA-GAACCATACCATTTTCAGCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGG-TGAAGAACCATACCATTTTCAGCC
EST: gi|5901292|gb|AW042392.1|AW042392
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|149000611|gb|EE037809.2|EE037809
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|6021590|gb|AW066518.1|AW066518
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGNGAAGAACCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|60354886|gb|DN221859.1|DN221859
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|148952074|gb|EC897865.2|EC897865
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|149095998|gb|EE181667.2|EE181667
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|22545963|gb|BU098322.1|BU098322
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|6056546|gb|AW090936.1|AW090936
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|149014157|gb|EE043702.2|EE043702
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|71429578|gb|DR810628.1|DR810628
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|148995931|gb|EE035174.2|EE035174
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC
EST: gi|5917336|gb|AW054127.1|AW054127
EST:     CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG                         TTGAGTGTATCCATTGAAGTTCCTGG-GAAGAACC-T--CATTTTCAGCCC
genomic: CTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCC

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), 49 (downstream exon)
Score: 505

GCATGACTACTACAACAGTGCCACAGAAGTGGTACTGACAATATTTGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 413

GCATGACTACTACAACAGTGCCACAGAAGTGGTACTGACAATATTTGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 676

GCATGACTACTACAACAGTGCCACAGAAGTGGTACTGACAATATTTGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 294

GCATGACTACTACAACAGTGCCACAGAAGTGGTACTGACAATATTTGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATGgtgtgttctg ... ctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttataattgtcttgtctgtttttactgtattcactaatcttgtttctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG
                               cactaat  putative branch site (score: 294)
                                     tcttgtttctcattct  CT-rich tract
                tgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttctgctcatattattattataattgtcttgtctgtttttactgtattcactaatcttgtttctcattctagTTGAGTGTATCCATTGAAGTTCCTGGTGAAGAACCATACCATTTTCAGCCCCGTCTGTTTTCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC