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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtcttctttgccctcatttagcagtagccgtattggtatcatcatgacctttgttggttcattttttttcattctttgcctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTGGGCACTTTGATTATTAACAAGCTTCGTGCAGGCATCAAG

Basic information

species Zea mays
transcript GRMZM2G458208_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 8
gtagtcttctttgccctcatttagcagtagc-cgtattggtatcatcatgacctttgttggttcattttttttcattctttgcctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTGGGCACTTTGATTATTAACAAGCTTCGTGCAGGCATCAAG
|||    | |||||  ||||  |  ||| |    |  ||||      |     ||| ||| |  |  |  |   |    |||||| | |||||| |||| |||||| ||||||||||| |||||||| || || || |||||||| ||| ||||||||||||||||||||||||||||||||
gta--tgtgtttgctttcataaaatagttgtatattgtggtggtgctactgattttcttgctataactggtca-acatcttgccttgcacagAAGCAAAGGCCTCTGCTGATTGTTGCTGAAGATGTAGAGAGCGAGGCATTGGGTACTCTGATTATTAACAAGCTTCGTGCAGGCATCAAG

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 8
gtagtcttctttgccctcatttagcagtagccgtattggtatcatcatgacctttgttggttcattttttttcattctttgcctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTGGGCACTTTGATTATTAACAAGCTTCGTGCAGGCATCAAG
|||      | |    ||| |  |    |     ||   ||    ||| |  |||  | |   |  || ||       ||||||    ||||  || | |||| ||||||||||||| |||||||||||||| |||||| ||| |||| | ||| | || ||||||||||| || ||||||
gtaagtgggtctttggtcaatcggattcaattagatctttacatgcatcaagtttagttgactacattgttc------ttgccttattcagACTCAGAGGCCTTTACTGATTGTTGCTGAAGATGTGGAAAGCGAAGCACTGGCCACTCTTATTCTAAATAAGCTTCGTGCTGGAATCAAG

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 7
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------------------------gtagtcttctttgccct-cattta-gcagtagccg--------tattggtatcat------catgacctttgttggttcattttttttcattctttgcctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTGGGCACTTTGATTATTAACAAGCTTCGTGCAGGCATCAAG
                                                                    |||| ||  |||    | |||  | | | |||  |         |||     |||      || || | |  |        |  |||   || | ||  | |  ||| | |||| |||||| ||||||||||| |||||||||||||||||||| ||||  ||  ||||  | || |||||| | |  ||  | |||
gcaagcaatcactgactttggtgcactgtttgaactttatttgccttctttaattttgttctcacctagtagactcttttcttgtacatacaagtaataggtgggggcatccatttaccacatgctatacacgaacctcctgataatgctagtttattttttctggtttgt-cagGATCAAAGGCCTCTCCTGATTGTTGCTGAAGATGTGGAAAGTGAAGCTTTGGCTACGCTGATAGTCAATAAGCTTAGGGGTGGTGTGAAG

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|33094209|gb|CF054203.1|CF054203
EST:     AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG                         AAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
genomic: AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAGgtagtcttct ... cctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
EST: gi|31357599|gb|CD441956.1|CD441956
EST:     AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG                         AAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
genomic: AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAGgtagtcttct ... cctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
EST: gi|61119163|gb|DN560124.1|DN560124
EST:     AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG                         AAACAAA-GCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
genomic: AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAGgtagtcttct ... cctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
EST: gi|31361464|gb|CD445821.1|CD445821
EST:     AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG                         AAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
genomic: AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAGgtagtcttct ... cctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
EST: gi|5499101|gb|AI854968.1|AI854968
EST:     AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG                         AAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
genomic: AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAGgtagtcttct ... cctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
EST: gi|67016113|gb|CO444862.1|CO444862
EST:     AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG                         AAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
genomic: AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAGgtagtcttct ... cctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
EST: gi|67023196|gb|CO451945.1|CO451945
EST:     AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG                         AAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG
genomic: AGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAGgtagtcttct ... cctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTG

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: 376

GAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAGgtagtcttct ... cctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTGGGCACTTTGATTATTAACAAGCTTCGTGCAGGCATCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 168

GAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAGgtagtcttct ... cctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTGGGCACTTTGATTATTAACAAGCTTCGTGCAGGCATCAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 192

GAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAGgtagtcttct ... cctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTGGGCACTTTGATTATTAACAAGCTTCGTGCAGGCATCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 265

GAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAGgtagtcttct ... cctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTGGGCACTTTGATTATTAACAAGCTTCGTGCAGGCATCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtatcatcatgacctttgttggttcattttttttcattctttgcctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTGGGCACTTTGATTATTAACAAGCTTCGTGCAGGCATCAAG
                        ttcattttttttcatt  CT-rich tract
                           attttttttcattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtcttctttgccctcatttagcagtagccgtattggtatcatcatgacctttgttggttcattttttttcattctttgcctggaacagAAACAAAAGCCTCTACTGATTGTTGCAGAAGATGTGGAAAGTGAAGCATTGGGCACTTTGATTATTAACAAGCTTCGTGCAGGCATCAAG

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