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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatgcttttcatccttgatgcaagttgccgagccaaagtgataagtttgagtgttttgttcgtgtcttgttgtaaatacgactgacaatgatctcctttttggcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGGCACCTAGTTCAGACTATTGTTCCAGGGACTAGATTAACTGTTGTTGGCA

Basic information

species Zea mays
transcript GRMZM2G075978_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 5
gttagatgcttttcatccttgatgcaagttgccgagccaaagtgataagtttgagtgttttgttcgtgtcttgttgtaaatacg-actgacaatgatctcctttttggcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGGCACCTAGTTCAGACTATTGTTCCAGGGACTAGATTAACTGTTGTTGGCA
||| | | ||   |||  |   | |  | |||   || |  ||  |     |  || | ||| |  | | |  ||   | |  | | | || | | | |   ||      |  |||||||||||||||||||||||| || |||||| ||||||| || ||||| ||||| || |||||||| |||||||| || ||||||||||||||  |||| |
gtttgttactg--cattatatgtcctcgctgcgatgctatggtttt----ctaggtttattggttatatgtccttaggatttagcaatcaccaagctgtatattacttggttaacagGATGTTCCAACTGGTGAGCTCCCGAGGAATATGCTGCTGTCCGTAGACAGGCATCTTGTTCAGACCATTGTTCCTGGAACTAGATTAACTGTAATTGGTA

upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 4
gttagatgcttttcatccttgatgcaagttgccgagccaaagtgataagtttgagtgttttgttcgtgtcttgttgtaaatacgactgacaatgatctcctttttggcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGGCACCTAGTTCAGACTATTGTTCCAGGGACTAGATTAACTGTTGTTGGCA
                  || || ||| ||   ||   ||| | | |  ||  ||    |   | |    |||   | |  || |     |||| | |  || |||        ||||||||||||||||||||||||| || ||  |||| || ||||| ||| | || || ||||||||  | || || ||  | ||||| ||  |  | || |
---------------gtattaatacaaatt--tgaataaaaataaaacattaaag----tcacttgaaaattgaaattataaccatatgtaatgctgtgattattga-------agGATGTTCCAACTGGTGAGCTTCCTAGAAACTTGCTTCTCTCTGTTGATCGACATCTGGTTCAGACAGTGGTACCTGGCTCAAGATTGACAATCATGGGAA
















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|87153503|gb|DY398292.1|DY398292
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211096879|gb|FL135596.1|FL135596
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211329963|gb|FL157736.1|FL157736
EST:     AGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211094408|gb|FL135586.1|FL135586
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|71429882|gb|DR810932.1|DR810932
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTG
EST: gi|32866416|gb|CF006098.1|CF006098
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211094409|gb|FL135587.1|FL135587
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211094411|gb|FL135589.1|FL135589
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTAGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|5555510|gb|AI881461.1|AI881461
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAA
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAA
EST: gi|211329958|gb|FL157731.1|FL157731
EST:     AGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211094402|gb|FL135580.1|FL135580
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211094412|gb|FL135590.1|FL135590
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGNAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211096881|gb|FL135598.1|FL135598
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211096877|gb|FL135594.1|FL135594
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|19058027|gb|BM736694.1|BM736694
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211091938|gb|FL135575.1|FL135575
EST:     AGAGCAAGNATGCGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211542713|gb|FK958380.1|FK958380
EST:     AGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211094413|gb|FL135591.1|FL135591
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTANATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211329962|gb|FL157735.1|FL157735
EST:     AGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211094414|gb|FL135592.1|FL135592
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211094403|gb|FL135581.1|FL135581
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211096880|gb|FL135597.1|FL135597
EST:     ANAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGANAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTANATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211094410|gb|FL135588.1|FL135588
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211329960|gb|FL157733.1|FL157733
EST:     AGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211329959|gb|FL157732.1|FL157732
EST:     AGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211096878|gb|FL135595.1|FL135595
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211094404|gb|FL135582.1|FL135582
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|149000777|gb|EE038000.2|EE038000
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGA-TGTGCTGCTTTCTGT
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGT
EST: gi|211091941|gb|FL135578.1|FL135578
EST:     ANAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211091939|gb|FL135576.1|FL135576
EST:     AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211094407|gb|FL135585.1|FL135585
EST:     AGAGCAAGTATGNGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
EST: gi|211094401|gb|FL135579.1|FL135579
EST:     AAAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAG                         GATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG
genomic: AGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGG

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), 42 (downstream exon)
Score: 209

CCTGGAGAGGAGCCATGCCCTCTGGACCCTTGGATTGCCGTTCCAGATAAGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGGCACCTAGTTCAGACTATTGTTCCAGGGACTAGATTAACTGTTGTTGGCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 38

CCTGGAGAGGAGCCATGCCCTCTGGACCCTTGGATTGCCGTTCCAGATAAGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGGCACCTAGTTCAGACTATTGTTCCAGGGACTAGATTAACTGTTGTTGGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 24

CCTGGAGAGGAGCCATGCCCTCTGGACCCTTGGATTGCCGTTCCAGATAAGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGGCACCTAGTTCAGACTATTGTTCCAGGGACTAGATTAACTGTTGTTGGCA


Block sizes: 42 (upstream exon), 40 (downstream exon)
Score: 16

CCTGGAGAGGAGCCATGCCCTCTGGACCCTTGGATTGCCGTTCCAGATAAGAGCAAGTATGTGGATCTCCAGACCCTCAAATTGCAAGAGAATCCTGAGgttagatgct ... gcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGGCACCTAGTTCAGACTATTGTTCCAGGGACTAGATTAACTGTTGTTGGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcgtgtcttgttgtaaatacgactgacaatgatctcctttttggcatctacagGATGTTCCAACTGGTGAGCTTCCAAGGAATGTGCTGCTTTCTGTAGATAGGCACCTAGTTCAGACTATTGTTCCAGGGACTAGATTAACTGTTGTTGGCA
                      gactgac  putative branch site (score: 16)
            ttgtaaata  TA-rich tract