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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgcttgcagcctgtatctgcagcttcattatctatctgtccaatgatatttttatatgcatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG

Basic information

species Zea mays
transcript GRMZM2G085670_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085670_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 3'ss of exon 5
gtaagatgcttgc-------agc-ctgtatctgcagcttcattatctatctgtccaatgatatttttatatgcatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG
|| |||||||||        ||  |  | |     | |||||| | || ||| | ||||||     || || |   ||| | | |    |||||||||||||| ||||||| |||||||||||||||||||| ||||| |||||||| |  |||||||||||
gtcagatgcttgttcttacaagtacattgttcatggtttcattgtttagctggcaaatgatccccctaaattctgtctgtacttgac--agGTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTG
















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|101398140|gb|EB820944.1|EB820944
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|93013201|gb|EB638721.1|EB638721
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|50325881|gb|CO521007.1|CO521007
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|101390708|gb|EB817288.1|EB817288
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927905|gb|CF032717.1|CF032717
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|71330909|gb|DR802251.1|DR802251
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927110|gb|CF031922.1|CF031922
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGC
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGC
EST: gi|211512615|gb|FL228208.1|FL228208
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTAC
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTAC
EST: gi|74236689|gb|DT644603.1|DT644603
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927326|gb|CF032138.1|CF032138
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|76936648|gb|DV174824.1|DV174824
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|211512612|gb|FL228205.1|FL228205
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|76294401|gb|DV033969.1|DV033969
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTA
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTA
EST: gi|89247571|gb|DY619357.1|DY619357
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32928013|gb|CF032825.1|CF032825
EST:     GGTATCGGCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|71423346|gb|DR806010.1|DR806010
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927322|gb|CF032134.1|CF032134
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|60359667|gb|DN226640.1|DN226640
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927333|gb|CF032145.1|CF032145
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcattatctatctgtccaatgatatttttatatgcatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG
                                             ttcgtttt  CT-rich tract
                   aatgatatttttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatgcttgcagcctgtatctgcagcttcattatctatctgtccaatgatatttttatatgcatactgcattcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC