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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctgtttgctctcatttaacggtaacagtattggttcattgtgggcctttgctgattctttttttttcattctttgcttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG

Basic information

species Zea mays
transcript GRMZM2G416120_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 8
gtattctgtttgctctcatttaacggtaacagtattg-gttcattgtgggcctttgctgattctttttttttcattctttgcttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG
||||  |||||||| ||||  ||  ||   | ||||| | |  |  |     ||| ||   | |   |  |  |    |||| | | |||||| ||||||||||| ||||||||||| |||||||| || || || ||||| |||||||||||||||||||||||||||||||||||||||
gtatg-tgtttgctttcataaaatagttgta-tattgtggtggtgctactgattttcttgctataactggtcaacatcttgccttgcacagAAGCAAAGGCCTCTGCTGATTGTTGCTGAAGATGTAGAGAGCGAGGCATTGGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG

upper sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 8
gtattctgtttgctctcatttaacggtaacagtattggttcattgtgggcctttgctgattctttttttttcattctttgcttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG
                     || |  |      ||  ||     ||    |||    |||  | |    | |  |||   |     |||| |||||||||| |||||||||| || || |||||||||||||| ||  | |  ||||| ||| | || || |||||||| || ||||||
---------------gtgagcaatgccattcactttattttgcactgactttttaaatattggtatcggctaacacttctttattgccagAGACAAAGGCCTTTACTGATTGTCGCTGAGGATGTGGAAAGTGATGCCCTTGCAACTCTTATTCTAAATAAACTTCGTGCTGGAATCAAG

upper sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 8
gtattctgtttgctctcatttaacggtaacagtattggttcattgtgggcctttgctgattctttttttttcattctttgcttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG
    |  ||  |   |   | ||  |  |    ||| | || ||    || |    |     |   |   |  ||||| || |    ||||  || |||||| ||||||||||||| |||||||||||||| |||||| | |  ||||| ||| | || ||||||||||| || ||||||
---gtaagtgggtctttggtcaatcg-gattcaattagatctttacatgcatcaagtttagttgactacattgttctt-gccttattcagACTCAGAGGCCTTTACTGATTGTTGCTGAAGATGTGGAAAGCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAG

upper sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------------------------gtattctgtttgctctcatttaacggtaacag-------tattggttcattgtgggcctt---------tgctgattctttttttttcattctttgcttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG
                                                                    |||  || ||| ||   |  ||   |||| ||        ||   || |      ||  |         | |||||  |  |  |||  || ||    |    ||| | ||||||||||| ||||||||||| |||||||||||||||||||| || | ||| |||||  | || |||||| | |  ||  | |||
gcaagcaatcactgactttggtgcactgtttgaactttatttgccttctttaattttgttctcacctagtagactcttttcttgtacatacaagtaataggtgggggcatccatttaccacatgctatacacgaacctcctgataatgctagtttattttttctggtttgtcagGATCAAAGGCCTCTCCTGATTGTTGCTGAAGATGTGGAAAGTGAAGCTTTGGCTACGCTGATAGTCAATAAGCTTAGGGGTGGTGTGAAG

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|50328354|gb|CO523480.1|CO523480
EST:     AAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAG                         AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTA
genomic: AAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAGgtattctgtt ... cttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTA
EST: gi|31349659|gb|CD434016.1|CD434016
EST:     GTTTTAGAAATGGCTCTAAAG                         AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
genomic: GTTTTAGAAATGGCTCTAAAGgtattctgtt ... cttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTA
EST: gi|71425566|gb|DR806758.1|DR806758
EST:     AAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAG                         AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTA
genomic: AAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAGgtattctgtt ... cttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTA
EST: gi|78078493|gb|DV506906.1|DV506906
EST:     TGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAG                         AAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTA
genomic: TGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAGgtattctgtt ... cttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTA
EST: gi|67019174|gb|CO447923.1|CO447923
EST:     AAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAG                         AAACAAAGGCCTCTACTGATTGTTGCAAAAGATGTGGAAAGTGAAGCATTG
genomic: AAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAGgtattctgtt ... cttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTA

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: 522

GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAGgtattctgtt ... cttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAGgtattctgtt ... cttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 273

GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAGgtattctgtt ... cttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 389

GAACTGGAAGACCCATTGATCTTAATTCATGACAAGAAAGTGACAAATATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTAAAGgtattctgtt ... cttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttcattgtgggcctttgctgattctttttttttcattctttgcttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG
                  tgctgat  putative branch site (score: 389)
              cctttgctgattcttt  CT-rich tract
                       attctttttttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctgtttgctctcatttaacggtaacagtattggttcattgtgggcctttgctgattctttttttttcattctttgcttggaacagAAACAAAGGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTAGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT