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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgagcaaatatgtctgaaaacatgtgatgcctcataatcagtggatctttgttcttttagccgacagcgttgcttaacaatttagttacttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG

Basic information

species Zea mays
transcript GRMZM2G375002_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G375002_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g58730.2 (Oryza sativa), 3'ss of exon 4
-tgtga-gcaaatatgtctgaaaacatgtgatgcctca--taatcagtggatctttgttcttttagccgacagcgttgcttaacaatttagttacttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG
 ||  |      | ||  |         |  ||| |    |||||| | |  | |  ||  | ||  |  | ||| |||||||| ||| |||||||  ||| ||||||||| ||||||||||| ||||| || ||||||||||||||||| || ||||||||||| |||
atgcaatattcttttgcttttctgttcattgtgcttttattaatcacttg--cgtacttgatgtaatc--cggcggtgcttaaccattaagttactgttaatagATCTGCGGGATGATAAGCAATTTTTCGTAGATCACCCTGGTGCTGTACCTATTTCCACTGCTCAG
















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|5055407|gb|AI734294.1|AI734294
EST:     TATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: TATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|6973662|gb|AW438236.1|AW438236
EST:     CTATGCTCCTGGCGTGCCCATAATCCTTGNTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: CTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|71302719|gb|DR787472.1|DR787472
EST:     CCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: CCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|16926993|gb|BM080061.1|BM080061
EST:     CCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: CCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|8383272|gb|BE056215.1|BE056215
EST:     TGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: TGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|67018898|gb|CO447647.1|CO447647
EST:     AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|16925708|gb|BM078776.1|BM078776
EST:     AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|5510771|gb|AI857155.1|AI857155
EST:     CGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: CGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|211356949|gb|FL222513.1|FL222513
EST:     AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|78107806|gb|DV526224.1|DV526224
EST:     AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|37391181|gb|CF632832.1|CF632832
EST:     AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|16918068|gb|BM073562.1|BM073562
EST:     AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATAATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|16925543|gb|BM078611.1|BM078611
EST:     CTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: CTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|28930831|gb|CB334192.1|CB334192
EST:     AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|28986594|gb|CB351213.1|CB351213
EST:     AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|101401925|gb|EB822590.1|EB822590
EST:     AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTG                         ATTTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
genomic: AAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAA
EST: gi|18174791|gb|BM350179.1|BM350179
EST:     GGCGTGCCCATAATCCTTGTTGGGACAAAAACTTG                         ATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCA
genomic: GGCGTGCCCATAATCCTTGTTGGGAC-AAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCA

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), 46 (downstream exon)
Score: 169

TTCTTGCATATTACCTGTGCATGTCGTTTTTTCCAGTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 196

TTCTTGCATATTACCTGTGCATGTCGTTTTTTCCAGTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 234

TTCTTGCATATTACCTGTGCATGTCGTTTTTTCCAGTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 150

TTCTTGCATATTACCTGTGCATGTCGTTTTTTCCAGTGGGTTCCTGAATTAAGGCACTATGCTCCTGGCGTGCCCATAATCCTTGTTGGGACAAAACTTGgtatgctctt ... cttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctttgttcttttagccgacagcgttgcttaacaatttagttacttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG
                            gcttaac  putative branch site (score: 150)
                              ttaacaatttagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgagcaaatatgtctgaaaacatgtgatgcctcataatcagtggatctttgttcttttagccgacagcgttgcttaacaatttagttacttgtaacagATCTGCGTGATGATAAGCAGTTTTTTGTTGATCACCCTGGTGCTGTTCCAATTTCCACTGCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT