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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctatattctttgttgataagttctcttctgtgaagcagattgatctaccatgcctaaccactcgccttctccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCAAAACCTCTTCTTTTGAAGAAACAACATCAGCAA

Basic information

species Zea mays
transcript GRMZM2G058910_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 14
gtctatattctttgttgata-----agttctcttctgtgaagcagattgatctacca-tgcctaaccactcgccttctccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCAAAACCTCTTCTTTTGAAGAAACAACATCAGCAA
|||  ||||| || ||| ||     | ||     || |||     | |  |  |  | | |  ||    || || | ||  |  ||||||||| |||||||||||||| | |||||||| || |||||| |||| ||||| ||  || | |||||||   | ||| ||| |
gtccgtattcgttattgttatgcagaattgcagactatgacatgaacttgtggataaatactaaaattttctccatttcttatgcagCTTGTTTTACTTCTGCTTGCTCTGGTGTCTGTTCCCTGGATGCTGATCCCAAAGCCATTTTTCTTGAAGATGGAGCATGAGCGA
















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|87156017|gb|DY400806.1|DY400806
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|71768892|gb|DR966829.1|DR966829
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|60397735|gb|DN230551.1|DN230551
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|33102453|gb|CF062413.1|CF062413
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|60396043|gb|DN228913.1|DN228913
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|22935878|gb|BU572153.1|BU572153
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|60351631|gb|DN218604.1|DN218604
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|71441347|gb|DR822397.1|DR822397
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|60352256|gb|DN219229.1|DN219229
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|26559777|gb|CA832012.1|CA832012
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAG-GGCCAGAAGACAG-GCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|87157808|gb|DY402597.1|DY402597
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|32919460|gb|CF024272.1|CF024272
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|26559615|gb|CA831850.1|CA831850
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|32846836|gb|CD986517.1|CD986517
EST:     CAGATGGTCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTGCCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|31359889|gb|CD444246.1|CD444246
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|32851026|gb|CD990707.1|CD990707
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|211366581|gb|FK956890.1|FK956890
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         STTGTTCTACTTSTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|22935980|gb|BU572255.1|BU572255
EST:     CAGATGATCTTAG-GAGAACCAG-TG-TTAGTGG-CAGAAGACAG-GCAG                         CTTGTTCTACTTCTGCTTGCTTTAG-GTCTGTACCTTGGATG-TGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|32850827|gb|CD990508.1|CD990508
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|67016167|gb|CO444916.1|CO444916
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
EST: gi|67013974|gb|CO442723.1|CO442723
EST:     CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAG                         CTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA
genomic: CAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 193

GTCGAAAGCAGATCTATACCACGTTATGATCTACATGTTCCTTAGCCCAACAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCAAAACCTCTTCTTTTGAAGAAACAACATCAGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 365

GTCGAAAGCAGATCTATACCACGTTATGATCTACATGTTCCTTAGCCCAACAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCAAAACCTCTTCTTTTGAAGAAACAACATCAGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 292

GTCGAAAGCAGATCTATACCACGTTATGATCTACATGTTCCTTAGCCCAACAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCAAAACCTCTTCTTTTGAAGAAACAACATCAGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 274

GTCGAAAGCAGATCTATACCACGTTATGATCTACATGTTCCTTAGCCCAACAGATGATCTTAGTGAGAACCAGTTGTTTAGTGGCCAGAAGACAGTGCAGgtctatattc ... tccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCAAAACCTCTTCTTTTGAAGAAACAACATCAGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgtgaagcagattgatctaccatgcctaaccactcgccttctccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCAAAACCTCTTCTTTTGAAGAAACAACATCAGCAA
                           gcctaac  putative branch site (score: 274)
                                 ccactcgccttctcc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctatattctttgttgataagttctcttctgtgaagcagattgatctaccatgcctaaccactcgccttctccaacacagCTTGTTCTACTTCTGCTTGCTTTAGTGTCTGTACCTTGGATGTTGATTCCAAAACCTCTTCTTTTGAAGAAACAACATCAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA