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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttgtatatttactcatgccgggtgcgcctactacatgctgatgtgatttactcatgcatgcatgcatatatatggtctcgctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCGGTGAAGGCCCGCGACTACTCCCGGTGGCCTGACAAGCCGGCGGCGTGGC

Basic information

species Zea mays
transcript GRMZM2G062396_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062396_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g56700.1 (Oryza sativa), 3'ss of exon 1
--------gttttgtatatttactcatgccgggtgcgcctactacatgctgatgtgatttactcatgcatgcatgcatatatatggtctcgct-ctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCGGTGAAGGCCCGCGACTACTCCCGGTGGCCTGACAAGCCGGCGGCGTGGC
         |   || ||    |||      |   || | | || ||  ||      |  | | |    |  |  | | || |   |   |   |  |||||| || |||||| | |||||||| ||||||||||||||||||||||||||||||||| ||||||||||||| |||||||| ||||||||||||| |||||
ttaaaacaatacagtgtacagtctctgtgtagtcacgtccaatatat-ttgtcagtttcaatttacagttttacacgtttagagtttactgtaacgtgcagGGTGAAGCGGTGAAAGACTGGCGGGAGATCGTGACCTACTTCTCGTACCCGGTGAAGTCCCGCGACTACTCGCGGTGGCCCGACAAGCCGGCGGGGTGGC

upper sequence: GRMZM2G062396_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0023g03370.t01 (Vitis vinifera), 3'ss of exon 1
------gttttg-tatatttactcatgccgggtgcgcctactacatgctgatgtgatttactcatgcatgcatgcatatatatggtctcg----ctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCGGTGAAGGCCCGCGACTACTCCCGGTGGCCTGACAAGCCGGCGGCGTGGC
      || |||   |  ||  |||||         | | ||||| |   ||||  |||  |     | | |  || ||   |  | ||        | |||||| || || ||||| |||||||| |||||||| ||||||||||| |||||  |     || | ||||||||  ||||||| |||||||| | || |||| 
ccttgggtcttggcctgatttttcatgttttac---ctttctacaagaaaatgtattttctttcatgaggaacccaaatggttactttcaaaattaattgcagGGAGAAGCAGTGCAAGACTGGCGCGAGATCGTAACCTACTTCTCCTACCCACTACGAACCAGGGACTACTCGAGGTGGCCAGACAAGCCAGAGGGGTGGA
















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|148993927|gb|EE033913.2|EE033913
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|91054735|gb|EB165153.1|EB165153
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|74233229|gb|DT641143.1|DT641143
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|89248480|gb|DY620266.1|DY620266
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|148958071|gb|EC904256.2|EC904256
EST:     ACATGTCGGGCGGGAAGAGGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCGG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|149000104|gb|EE037223.2|EE037223
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|76289196|gb|DV028764.1|DV028764
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|71766105|gb|DR964042.1|DR964042
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|71433943|gb|DR814993.1|DR814993
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|71426562|gb|DR807612.1|DR807612
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|211061165|gb|FL093049.1|FL093049
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|78115224|gb|DV533612.1|DV533612
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|149102091|gb|EE287547.2|EE287547
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|211061161|gb|FL093045.1|FL093045
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|149047712|gb|EE048196.2|EE048196
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
EST: gi|148953974|gb|EC899363.2|EC899363
EST:     ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAG                         GGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG
genomic: ACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCG

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: 21 (upstream exon), 33 (downstream exon)
Score: 3

CCTCGCGCGCGACTTCTTCGCGCTCCCGCCCGAGGACAAGCTCCGCTTCGACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCGGTGAAGGCCCGCGACTACTCCCGGTGGCCTGACAAGCCGGCGGCGTGGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 284

CCTCGCGCGCGACTTCTTCGCGCTCCCGCCCGAGGACAAGCTCCGCTTCGACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCGGTGAAGGCCCGCGACTACTCCCGGTGGCCTGACAAGCCGGCGGCGTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

CCTCGCGCGCGACTTCTTCGCGCTCCCGCCCGAGGACAAGCTCCGCTTCGACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCGGTGAAGGCCCGCGACTACTCCCGGTGGCCTGACAAGCCGGCGGCGTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1207

CCTCGCGCGCGACTTCTTCGCGCTCCCGCCCGAGGACAAGCTCCGCTTCGACATGTCCGGCGGGAAGAAGGGCGGCTTCATCGTCTCCAGCCACCTCCAGgttttgtata ... gctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCGGTGAAGGCCCGCGACTACTCCCGGTGGCCTGACAAGCCGGCGGCGTGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctgatgtgatttactcatgcatgcatgcatatatatggtctcgctctcgcagGGGGAGGCGGTGCAGGACTGGCGTGAGATCGTGACCTACTTCTCGTACCCGGTGAAGGCCCGCGACTACTCCCGGTGGCCTGACAAGCCGGCGGCGTGGC
 tgctgat  putative branch site (score: 1207)
                                         tctcgctctc  putative PPT
                               atatatat  TA-rich tract