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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatggctttttgttgattttcacttgtgttggtagctgttgatttctgttgcatcgattatccttgattttgtgttgtttactggtt...

Basic information

species Zea mays
transcript GRMZM2G058498_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os08g07960.1 (Oryza sativa), 5'ss of exon 9
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatggctttttgttgattttcacttgtgttggtagctg---ttg-atttctgttgcatcgattatcct-tgattttgtgttgt--ttactggtt
|| |||||||| ||||||||||||||||| || || || || || |||||||||||||||||||| || || || |||||      || |   ||||| ||| |  | || || ||||  ||||   ||   ||| |||| |||| | | || ||| |  |||||||   | ||  | | || ||
GTTCATCACACGTTTGCAACTGCTGGATCAGATGGCGCATTTAATTTCTGGGATAAGGATAGCAAACAAAGACTGAAGgt---ttgatgt---tggctcttt-tgaagttccatttgtactggttattgcacttgtatttttgttcccttgagtattcagtgatttttaatagtcataattgctt

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA15G05740.1 (Glycine max), 5'ss of exon 8
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatgg----ctttttgttgattttcacttgtgttggtagctgttgatttctgttgcatcgattatccttgattttgtgttgtttactggtt---------
|| || ||||||||||||||| |||| ||||| ||||||||||| || |||||||||||||| || |||||||| |||||    | ||||  ||      |||    |  ||  | |||        | | ||   || | | | ||||  ||||  | || || | |  ||   ||| ||          
GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGGGATAAGGATAGTAAACAGAGGCTCAAGgttattccatttttattaaacacttccattcaatcctaactgacacatattgttgc-aatatttttggcat-aatta--catgcttatctaatgcaaacttgtcttatttcag

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G13780.1 (Glycine max), 5'ss of exon 8
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatggc---tttttgttgattttcacttgtgttggtagctgttgatttctgttgcatcgattatccttgattttgtgttgtttactggtt
|| |||||||| |||||||||||||||||||| |||||||| || |||||||||||||| || || ||||| || |||||       ||||  |       | || |    | ||  ||   |  | | ||| |  ||    || |    |  || |||  |||| | |||| || |    
GTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAGGACAGTAAACAGAGACTCAAGgtttcttgctttctctattacactcttctcacctgtcctttccttctgaaactgatctttggaatttc-caaaacatacttt-tttttttttgtatagtata-

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G19260.1 (Glycine max), 5'ss of exon 8
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatgg----ctttttgttgattttcacttgtgttggtagctgttgatttctgttgcatcgattatccttgattttgtgt---tgtttactggtt---
|| || ||||||||||||||| |||| ||||| ||||||||||| || |||||||||||||| || ||| |||| |||||    | ||||  ||      |||    |  |||   |              |  |||| | | | ||||          | || |  ||     || |  || ||   
GTACACCACACATTTGCAACTTCTGGTTCTGATGGTGCTTTCAATTTTTGGGATAAGGATAGTAAACAGCGGCTCAAGgttattccatttttattaaacacttccattcaattcctaaccaacacatattgtagtgatatttttggcataatcacatgcttatctaatgcaaacgtgtcttgtttcag

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA01G09290.1 (Glycine max), 5'ss of exon 8
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatggctttttgttgattttcacttgtgttggtagctgttgatttctgttgcatcgattatccttgat---tttgtgttgtttactggtt-
|| |||||||| |||||||||||||||||||| |||||||| || ||||||||||| || || || ||||| || |||||   |   ||||  |   |  |      || |||| |||  |  |  ||  |||   ||| |   | || | |||   |     ||||||| |||  |  || 
GTACATCACACTTTTGCAACTGCTGGATCTGATGGTGCTTTTAATTTCTGGGATAAAGACAGTAAACAGAGACTCAAGgttc-ctgctttctctaattaatacactcttctcacctgtcct--ttccttctgaaa-ctgatctttggaatttccaaaacatacttgtgttttttttttattt

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 9
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatggctttttgttgattttcacttgtgttggtagctgttgatttctgttgcatcgattatccttgattttgtgttgtttactggtt
|| |||  ||| |||||||||||||| || || ||||||||||| |||||||| || ||||| || || || || ||||||      ||| | |     |   ||||||||   || | ||| || |     | || | |  ||       |  |  ||| |||||     || |   
GTACATGGCACTTTTGCAACTGCTGGGTCAGATGGTGCTTTCAATTTCTGGGACAAAGATAGTAAACAAAGACTCAAGgta------ttttcct---cctgcattgatttt---ttattttgttaaccaagtaattatctaaca------gttttgtattctgtgtc-cccacag---

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv09s0002g09150.t01 (Vitis vinifera), 5'ss of exon 8
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtaga--ccaatttccatggctttttgttgattttcacttgtgttggtagctgttgatttctgttgcatcgattatccttgattttgtgttgtttactggtt
|| ||||| |||||||||||||| || ||||| |||||||| || || ||||| |||||||| || ||||| || |||||     |||| | |  |   ||||||   |||||  |  ||  || ||  | |   |||  ||||   |  | || | |||  |   |||  |   |   |
GTGCATCATACATTTGCAACTGCAGGGTCTGATGGTGCTTTTAATTTTTGGGACAAGGATAGTAAACAGAGACTTAAGgtgcctcccaaatactttcagtttttgaatattttt-cccgttctgttatttctgtgttttagttgtcact-tcatacatgaactatcgttcctggtttcat

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 9
lower sequence: Vv12s0055g00900.t01 (Vitis vinifera), 5'ss of exon 9
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatggctttttgttgattttcacttgtgttggtagctgttgatttctgttgca--tcgattatccttgattttgtgttgtttac--tggtt---
|| |||||||||||||| ||||| || |||||||||||||| || |||||||| |||||||| || ||||| || ||||||     || || | |  |  || |||| | |   || |  | || | | | |    ||||| |   || ||||| || |||| | |  | |||||  |  |    
GTGCATCACACATTTGCCACTGCAGGCTCTGACGGTGCTTTTAATTTCTGGGACAAGGATAGTAAACAGAGACTCAAGgta-----atctcaaggattcctttttgaatat--gttcttctcgttgttttcggacactgttactcttctattattctagattctattgtttttaccctaatcgga

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ25923 (Selaginella moellendorffii), 5'ss of exon 8
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatggctttttgttgattttcacttgtgttggtagctgttgatttctgttgcatcgattatccttgattttgtgttgtttactggtt
||   |   ||||| || ||  | || ||||| |||||||| ||||||||||| ||||| |||||||||||||| ||||||||   |||| ||    | ||||||| | |      |||  | || || |   |||||    ||                                  
GTGTTTGGAACATTCGCTACATCAGGCTCTGATGGTGCTTTTAACTTCTGGGACAAGGACAGCAAGCAGAGGCTCAAGgtaga---attttcactcttctttgttggtgtgtttcggtgc-gttatctttctttttct-ccacag---------------------------------

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 9
lower sequence: EFJ10886 (Selaginella moellendorffii), 5'ss of exon 8
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatggctttttgttgattttcacttgtgttggtagctgttgatttctgttgcatcgattatccttgattttgtgttgtttactggtt
||   |   ||||| || ||  | || ||||| |||||||| ||||||||||| ||||| |||||||||||||| ||||||||   |||| ||    | ||||||| | |      |||  | || || |   |||||    ||                                  
GTGTTTGGAACATTCGCTACATCAGGCTCTGATGGTGCTTTTAACTTCTGGGACAAGGACAGCAAGCAGAGGCTCAAGgtaga---attttcactcttctttgttggtgtgtttcggtgc-gttatctctctttttct-ccacag---------------------------------

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|71310172|gb|DR791375.1|DR791375
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|5055819|gb|AI734706.1|AI734706
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|548062|gb|T25262.1|T25262
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTNTTAGTAGATGCCCC-TTCCCATTCCTTGGCAGTACCTTC
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTG-CAGTACCTTC
EST: gi|32823928|gb|CD963650.1|CD963650
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|32838237|gb|CD977915.1|CD977915
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGT
EST: gi|78092604|gb|DV520978.1|DV520978
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|24769686|gb|CA404815.1|CA404815
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|50339683|gb|CO534809.1|CO534809
EST:     CTGACGGTGC-TT-AACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|71756690|gb|DR954627.1|DR954627
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|12969344|gb|BG266288.1|BG266288
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTTTTAGTAGATGCCCCCTTCCCATTCCCTGCAGTACCTTCAACAGTGAT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|211462818|gb|FL454180.1|FL454180
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|78023897|gb|DV492284.1|DV492284
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|67013709|gb|CO442458.1|CO442458
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
EST: gi|32945537|gb|CF050356.1|CF050356
EST:     CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAG                         GCTNTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT
genomic: CTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 239

GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 235

GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 165

GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 131

GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaat ... ttctgtacagGCTTTTAGTAGATGCCCCCTTCCCATTCCTTGCAGTACCTTCAACAGTGATGGTTCCATATTTGCTTATGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCATCACACATTTGCAACTGCTGGATCTGACGGTGCTTTCAACTTCTGGGATAAGGATAGCAAGCAGAGGCTAAAGgtagaccaatttccatggctttttgttgattttcacttgtgttggtagctgttgatttctgttgcatcgattatccttgattttgtgttgtttactggtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG