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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtgctctctgccttgtccaactttgcacccgtcccctctagagggatctcccaagttttaactcttcctcttgcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACCAGCACGATCACTGTGGTCCTGTTTAGCACTATG

Basic information

species Zea mays
transcript GRMZM2G027851_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027851_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 12
-------------------------------------------gttcgtgctctctgccttgtccaactttgcacccgtccc------------ctctagagggatctcccaagttttaactcttcctcttgcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACCAGCACGATCACTGTGGTCCTGTTTAGCACTATG
                                            |  ||  |      ||  ||   |  |  |   |||||               |||     |||||  |   |||||| |  |  |||||| ||||||| || |||||||| || ||| ||||||||||||| || ||||||||||||||||| |||||||| || || ||||||||||||
gtcagtccgtcagtgcaagactattgcttcacaccatctgtatatctgtatttctcttctcatcttgccattaattagtcccaggagaagtatgtcttagtttcttctccttaagcttaactgtctcg-ttgcaattgcagTTTACAAGATCTGGCCATACTCAGCTGCACGGCAATGCAATAATGATCACCAGCACCATCACTGTCGTTCTTTTTAGCACTATG

upper sequence: GRMZM2G027851_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g47100.3 (Oryza sativa), 3'ss of exon 13
-------------------------------------------gttcgtgctctctgccttgtccaactttgcacccgtccc------------ctctagagggatctcccaagttttaactcttcctcttgcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACCAGCACGATCACTGTGGTCCTGTTTAGCACTATG----------------
                                            |  ||  |      ||  ||   |  |  |   |||||               |||     |||||  |   |||||| |  |  |||||| ||||||| || |||||||| || ||| ||||||||||||| || ||||||||||||||||| |||||||| || || ||||||||||||                
gtcagtccgtcagtgcaagactattgcttcacaccatctgtatatctgtatttctcttctcatcttgccattaattagtcccaggagaagtatgtcttagtttcttctccttaagcttaactgtctcg-ttgcaattgcagTTTACAAGATCTGGCCATACTCAGCTGCACGGCAATGCAATAATGATCACCAGCACCATCACTGTCGTTCTTTTTAGCACTATGGTGAGTCATCTTACTG
















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|93281413|gb|EB673677.1|EB673677
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|50333104|gb|CO528230.1|CO528230
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|89755588|gb|DY685957.1|DY685957
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|93282180|gb|EB674444.1|EB674444
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|71437105|gb|DR818155.1|DR818155
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|74238598|gb|DT646512.1|DT646512
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|78093452|gb|DV521826.1|DV521826
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|71760181|gb|DR958118.1|DR958118
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|71761590|gb|DR959527.1|DR959527
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|88750196|gb|DY534337.1|DY534337
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|71446906|gb|DR827956.1|DR827956
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCG
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCG
EST: gi|71758416|gb|DR956353.1|DR956353
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|78074782|gb|DV503216.1|DV503216
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|26455862|gb|CA827445.1|CA827445
EST:     GGACTGATGAGAGGTGCCG-GTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|93281414|gb|EB673678.1|EB673678
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|37382323|gb|CF628103.1|CF628103
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|76013009|gb|DT940179.1|DT940179
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|76293702|gb|DV033270.1|DV033270
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|74239374|gb|DT647288.1|DT647288
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|19770144|gb|BQ034865.1|BQ034865
EST:     GTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|71427238|gb|DR808288.1|DR808288
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|78115472|gb|DV533860.1|DV533860
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|37399694|gb|CF637180.1|CF637180
EST:     GGGCCGGAATGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACAATGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|71760562|gb|DR958499.1|DR958499
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|71440636|gb|DR821686.1|DR821686
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
EST: gi|78080129|gb|DV508541.1|DV508541
EST:     GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAG                         TTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC
genomic: GGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACC

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: 158

ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACCAGCACGATCACTGTGGTCCTGTTTAGCACTATG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 53

ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACCAGCACGATCACTGTGGTCCTGTTTAGCACTATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 35

ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACCAGCACGATCACTGTGGTCCTGTTTAGCACTATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 74

ATTGTAATATGGTGGGCCGGACTGATGAGAGGTGCCGTGTCCATTGCTCTCGCTTACAACAAGgttcgtgctc ... gcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACCAGCACGATCACTGTGGTCCTGTTTAGCACTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccgtcccctctagagggatctcccaagttttaactcttcctcttgcaactgcagTTCACGAGATCTGGACACACTGAGCTGCACGGCAACGCGATAATGATCACCAGCACGATCACTGTGGTCCTGTTTAGCACTATG
                            ttttaac  putative branch site (score: 74)
                                  ctcttcctcttgc  CT-rich tract
                         aagttttaa  TA-rich tract