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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatagtgaattaattcatgcgctgtacttttttttatacttcttgaagagcatttctagctcactctatggtatctgttgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAA

Basic information

species Zea mays
transcript GRMZM2G078033_T01
intron # 5
splice site 3'
intron type U2

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|19350869|gb|BM895401.1|BM895401
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGCGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA
EST: gi|71434451|gb|DR815501.1|DR815501
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGATGAGCAGGAACACGACA
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACA
EST: gi|71437088|gb|DR818138.1|DR818138
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGATGAGCA
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCA
EST: gi|149101926|gb|EE287458.2|EE287458
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCCTGAAGAG                         ACCGTGAAAGTGCGCGATGAG
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAG
EST: gi|67021466|gb|CO450215.1|CO450215
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACTGGCA
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA
EST: gi|148932442|gb|EC876155.2|EC876155
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGAT
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGAT
EST: gi|31359211|gb|CD443568.1|CD443568
EST:     AGGAGACAGTCGATAAAGCTGGAGAAACATTCCAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGATGAGCAGGAACACCACATGCCCCTGCTACAGGCA
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA
EST: gi|149011847|gb|EE042454.2|EE042454
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA
EST: gi|211397302|gb|FL135062.1|FL135062
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA
EST: gi|31364427|gb|CD448782.1|CD448782
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA
EST: gi|148950453|gb|EC896022.2|EC896022
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGAT
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGAT
EST: gi|148981924|gb|EE027991.2|EE027991
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGATGAGCA
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCA
EST: gi|91055202|gb|EB165620.1|EB165620
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGATG
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATG
EST: gi|148953295|gb|EE152782.2|EE152782
EST:     GGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTTGA-GAG                         ACGGTGAAAGTGCGCGATGAGCAG
genomic: GGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTT-GAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAG
EST: gi|67012438|gb|CO441187.1|CO441187
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA
EST: gi|149011840|gb|EE042447.2|EE042447
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGGGAAAGTGCGCGATGA
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGA
EST: gi|149047179|gb|EE048186.2|EE048186
EST:     AGGAGACCGTCGATAAAGTTGGAGAAACATTCCAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGATGAGCAGGAACCCGACCTGCC
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCC
EST: gi|211527782|gb|FL304403.1|FL304403
EST:     AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAG                         ACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGGCACTGCTACAGGCA
genomic: AGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCA

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: 253

CTATGCTCTCTTTGATAAGGATGGTAATCAGGTCCCAAAGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 610

CTATGCTCTCTTTGATAAGGATGGTAATCAGGTCCCAAAGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

CTATGCTCTCTTTGATAAGGATGGTAATCAGGTCCCAAAGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 418

CTATGCTCTCTTTGATAAGGATGGTAATCAGGTCCCAAAGGAGACAGTCGATAAAGTTGGAGAAACATTCGAGAGAATTCTTGAAGAGgtacatagtg ... tgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatacttcttgaagagcatttctagctcactctatggtatctgttgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAA
                        agctcac  putative branch site (score: 418)
                  atttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatagtgaattaattcatgcgctgtacttttttttatacttcttgaagagcatttctagctcactctatggtatctgttgcatcacagACGGTGAAAGTGCGCGATGAGCAGGAACACGACATGCCACTGCTACAGGCAATTTCTATTGTGTTTGAGAGGCACCCCCATCTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG