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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttattcaccttttattttatcagacaatatgacattccattttgtgacgaggatctacaacaattgtgaagaagcagtccttcaacagcgtgtttcaatcatatactattgtttttttcacatgtactcatttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA

Basic information

species Zea mays
transcript GRMZM2G058910_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os03g14690.1 (Oryza sativa), 3'ss of exon 13
gtaagtttattcaccttttattttatcagacaatatgacattccattttgtgacgaggatctacaacaattgtgaagaagcagtccttcaacagcgtgtttcaatcatatactattgtttttttcacatgtactcatttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA
                                 || |   |    | | |||  ||    |        || || |  | |  | |||  | |     ||   | || ||  |||| | | || |   ||||  | |||| ||||||||||||||||| |||||||||||||||||||||||||||||||| ||| | ||| ||||||| ||||| |||||| |||||||| | ||||||||||| 
--------------------------------gtaagtt-tattgtctcgtgttgaatgccctt-----ttatgtaaca-ctctactttgagatgagattatgaccagat--tattctctattgctgctgtatgcttttgtaacagGTACCAGTTCATCCCCCAGCTGATCTTCTTGAACAGCTTATTTGGTTACTTATCCATGCTCATCATTATCAAGTGGAGCACGGGGGCAAAAGCAGATCTG

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA06G03040.1 (Glycine max), 3'ss of exon 13
gtaagtttattcaccttttattttatcagacaatatgacattccattttgtgacgaggatctacaacaattgtgaagaagcagtccttcaacagcgtgtttcaatcatatactattgtttttttcacatgtactcatttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA
                                                 || |     |   |||||  | ||  | | | |     ||    | || |     ||||   | |||| |||||  |    | |          ||||||||||||| |||||||| | || ||||| |||||||| ||||||||||| ||  | ||||| ||||| || ||| |||| |||||  | || || || 
-------------------------------------------------gtaatagcaaaaaacaactttagttta-atgaacattgtctgtggtgtatggtgttcat---caattggtttttcgatg-atgcct--------cagGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTACCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCACAGGCTGACCTG

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA04G03010.1 (Glycine max), 3'ss of exon 14
gtaagtttattcaccttttattttatcagacaatatgacattccattttgtgacgaggatctacaacaattgtgaagaagcagtccttcaacagcgtgtttcaatcatatactattgtttttttcacatgtactcatttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA
                                               |  |  | |  | | ||  || ||      | |  ||      |  | || |     ||||     |||| ||||   |   |  ||||         ||||||||||| |||||||| | || ||||| |||||||| |||||||| || ||  | ||||| ||||| || ||| |||| |||||| | || || || 
----------------------------------------------gtaatagcaaaaaacaacttcagtttaatgaacgtggtgt----atggtgtatggtgttcat---taattggttttccgatgaggcctca---------gGTACCAGTTCGTTCCCCAGATAATATTCTTAAACAGCTTGTTTGGCTATCTTTCACTCCTCATAATTATAAAATGGAGCACTGGGTCGCAGGCTGACCTG

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT2G21410.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagtttattcaccttttattttatcagacaatatgacattccattttgtgacgaggatctacaacaattgtgaagaagcagtccttcaacagcgtgtttcaatcatatactattgtttt-tttcacatgtactcatttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA
                                                || |      || | |  |  |||| |  | | | | || | |    ||  |||||| || | |  |||| |  | |||||||      ||     ||||| ||||||| |||||||| |||| ||||||||| |||| |||||||| || ||  | ||||| || || ||||||||||| || ||  |||||||| ||
-----------------------------------------------gtgagtattcaattttctgcccttgtcattacgtacttctccca----gttcttcaattatctgcccttgtctgatctcacatg-----gttc----cagGTTCCAGTTCGTTCCCCAGATGATATTCTTGAACTGCTTGTTTGGCTATCTTTCGGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTA

upper sequence: GRMZM2G058910_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT4G39080.1 (Arabidopsis thaliana), 3'ss of exon 13
gtaagtttattcaccttttattttatcagacaatatgacattccattttgtgacgaggatctacaacaattgtgaagaagcagtccttcaacagcgtgtttcaatcatatactattgtttttttcacatgtactcatttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA
                                   | |  |   ||||| |||| |     | |      | |    |     ||||| |||||      ||| ||||     ||       |  |  | | |    |||   ||||| |||||||||||||||  |||| |||||||||||||| |||||||| || ||  | ||||| || || ||||||||||| || ||  |||||||| | 
-----------------------------gtgggttcagttgatattttctgaccatagcgtgctctctctctctccagt---tccttaaacagtaaaaatcagtcat----catctcagcatctaattttgcgggcttg---cagGTTCCAGTTCATTCCCCAAATGATATTCTTGAACAGCTTGTTTGGCTATCTCTCAGTCCTCATCATCATAAAGTGGTGCACTGGTTCTCAAGCAGATTTG

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|71768892|gb|DR966829.1|DR966829
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|60397735|gb|DN230551.1|DN230551
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|60396043|gb|DN228913.1|DN228913
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|22935878|gb|BU572153.1|BU572153
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|60351631|gb|DN218604.1|DN218604
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|71441347|gb|DR822397.1|DR822397
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|60352256|gb|DN219229.1|DN219229
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|87157808|gb|DY402597.1|DY402597
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|32919460|gb|CF024272.1|CF024272
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|26559615|gb|CA831850.1|CA831850
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|211366581|gb|FK956890.1|FK956890
EST:     TTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCARCTGATCTTCTTGAACATCTTATTTGGCTACCT
genomic: TTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|67016167|gb|CO444916.1|CO444916
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|67013974|gb|CO442723.1|CO442723
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
EST: gi|30031855|gb|CB833706.1|CB833706
EST:     GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTG                         GTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT
genomic: GTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCT

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), 47 (downstream exon)
Score: 193

AGATGAAGATGTCGATTCTTCTTGGAGTTGCACAAATGAACCTTGGGATTGTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 356

AGATGAAGATGTCGATTCTTCTTGGAGTTGCACAAATGAACCTTGGGATTGTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

AGATGAAGATGTCGATTCTTCTTGGAGTTGCACAAATGAACCTTGGGATTGTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 398

AGATGAAGATGTCGATTCTTCTTGGAGTTGCACAAATGAACCTTGGGATTGTGATTAGTTACTTCAATGCAAAATTTTTCAGGAACAGTATTAATGTGTGgtaagtttat ... tttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagcgtgtttcaatcatatactattgtttttttcacatgtactcatttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA
                                         ctcattt  CT-rich tract
           aatcatatactattgt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttattcaccttttattttatcagacaatatgacattccattttgtgacgaggatctacaacaattgtgaagaagcagtccttcaacagcgtgtttcaatcatatactattgtttttttcacatgtactcatttgaaacagGTACCAGTTCATTCCCCAGCTGATCTTCTTGAACAGCTTATTTGGCTACCTGTCCTTGCTCATTATTATTAAGTGGTGCACGGGGTCGAAAGCAGATCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT