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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctgcttcactgctgtttgaattgcttgtcgacttggcaattggctcccagtcgctggtacgtgggcacgtggccatgcctgtaaaggggagatgcgcactaactggacgggatttgcaatggtgtgtgctgttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTGTGTTCTCGGACCCATACCGTGTTTCCAAATTTAATCGGTGGACCTCGCC

Basic information

species Zea mays
transcript GRMZM2G464137_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G464137_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g57400.1 (Oryza sativa), 3'ss of exon 2
gtgagctgcttcactgct---gtttgaattgcttgtcgacttggc----aattggctcccagtcgctggtacgtgggcacgtggccatgcctgt-aaaggggagatgcgcactaactggacgggatttgcaatggt-gtgtgctgttg-ttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTGTGTTCTCGGACCCATACCGTGTTTCCAAATTTAATCGGTGGACCTCGCC
||  | || || | |      |||||  |||| |||  |   ||     |||  |  || | | | | | | || |    ||  |  || || | ||| ||||||       ||||   |  |    || |||| | |||| ||||    |||||||||| ||||||  |  || |||||||||||||||||||| |||||||| |||||||| |||||||||    |  ||||||  ||||| || || || ||
gttggttgatttattatacaggtttggtttgcctgtgaaaagggagaaaaatgagaaccaaattgatagaatgttg---tgtt-ctgtgactatgaaaagggagaaaaatgataaccaaattga---tggaatgtttgtgttctgtgaactgcagTTGCTCAGTACTGCGATAATGTGGAGATGTGTAGGCTCACAGAGCAAGTCGTGTTCTCAGACCCATACATGCTCGCCAAATACAATCGTTGCACATCACC

upper sequence: GRMZM2G464137_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT1G49820.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagctgcttcactgctgtttgaattgcttgtcgacttggcaattggctcccagtcgctggtacgtgggcacgtggccatgcctgtaaaggggagatgcgcactaactggacgggatttgcaatggtgtgtgctgttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTGTGTTCTCGGACCCATACCGTGTTTCCAAATTTAATCGGTGGACCTCGCC
                                                            | |       | |    | ||     | |   |   |||     || |  |  |    | |  |  || | |  ||||  || |||  |  | |  | ||  || |||||| | ||  |  | ||||||||||||||||| |||||||||||  | ||||||| ||||||||| ||||| || ||
------------------------------------------------------------gttcaaaaccctcacatctattttatttactagtcaatgt----tatcgtgttgcttgtagtgagtgtcttttgtgtttgtgtagTAACCGAATTTTGTGGTAATGTGGAGTTATGCCGATTAACGGAGCAAGTTGTGTTTTCGGACCCATATAGAGTTTCCACATTTAATCGTTGGACTTCACC
















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|76925788|gb|DV170594.1|DV170594
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|148931973|gb|EC875233.2|EC875233
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|148962543|gb|EE013418.2|EE013418
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|71432514|gb|DR813564.1|DR813564
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|148969592|gb|EE020430.2|EE020430
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|76913361|gb|DV165093.1|DV165093
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|76292759|gb|DV032327.1|DV032327
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|78114422|gb|DV532811.1|DV532811
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|76011769|gb|DT938939.1|DT938939
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|149048896|gb|EE048395.2|EE048395
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|148930196|gb|EC872600.2|EC872600
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|148938568|gb|EC882889.2|EC882889
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|149080185|gb|EE169203.2|EE169203
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|149100125|gb|EE186180.2|EE186180
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
EST: gi|71430317|gb|DR811367.1|DR811367
EST:     CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAG                         TTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG
genomic: CTTCTTCACCTCCCTCCTCTATAACAATACCACGGATCATAAGAACGGAGgtgagctgct ... gttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggagatgcgcactaactggacgggatttgcaatggtgtgtgctgttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTGTGTTCTCGGACCCATACCGTGTTTCCAAATTTAATCGGTGGACCTCGCC
           cactaac  putative branch site (score: 1)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctgcttcactgctgtttgaattgcttgtcgacttggcaattggctcccagtcgctggtacgtgggcacgtggccatgcctgtaaaggggagatgcgcactaactggacgggatttgcaatggtgtgtgctgttgttgcagTTGCTAAGTACTCTGCGAACGTGGAGATGTGTAGGCTCACGGAGCAAGTTGTGTTCTCGGACCCATACCGTGTTTCCAAATTTAATCGGTGGACCTCGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA