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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttccacctgttcttgctgtgtgactgtgtcgccttccttggttgttttacttttatgcactgtcccggagcggcggaaacgattaatgacaatt...

Basic information

species Zea mays
transcript GRMZM2G176029_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G176029_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g39260.1 (Oryza sativa), 5'ss of exon 3
CAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttccacctgttct--tgctgtgtgactgtgtcgccttccttggttgttttacttttatgcactgtcccggagcggcggaaacgattaatgacaatt-
| |||| ||| |  |||||||||||||||||||| ||||||| ||  |||| ||| |||||||||||||||| ||||||| |||||||||||| |||||||| ||||| || |||  ||  ||  || |  ||  |    |||  ||| |   |  | |||| ||||   |   | | | |   ||     |  |  || || 
CCGCGCGCCGCTGCGGAAGTACTGGGGCGTCAGCATCACCAACACTGTCGGCCCGGCCATGGGGATCGAGGCGCTCAAGTTCATCAGCTACCCAGCTCAGgtttggttgcagctgcccttttgtcgtctcgcttcgcttgctttgttgctctatgcatttttgtgcagc-tattgtatctgt--aattagatgtttccatttt
















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|78118465|gb|DV536850.1|DV536850
EST:     GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTGGCAAAATCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG
EST: gi|211352183|gb|FL343466.1|FL343466
EST:     GCCGACCATGGGGATCGAGGCTCTTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTGGCAAAAATTCTTCTAAGATGATTCC
genomic: GCCGACCATGGGGATCGAGGCTCT-CAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAA-T-CTTCTAAGATGATTCC
EST: gi|148931883|gb|EC877348.2|EC877348
EST:     GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTGGCAAAATCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG
EST: gi|149005383|gb|EE039935.2|EE039935
EST:     GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTGGCAAAATCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG
EST: gi|148977669|gb|EE026096.2|EE026096
EST:     GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTTGGCAAA-TCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTT-GGCAAAATCTTCTAAGATGATTCCTG
EST: gi|78080957|gb|DV509369.1|DV509369
EST:     GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTGGCAAAATCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG
EST: gi|148985614|gb|EE029715.2|EE029715
EST:     GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTGGCAAAATCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG
EST: gi|94479889|gb|EB708847.1|EB708847
EST:     GGCCGACCATGGGGATCCAGGCTCTCAAGTACCTCAGCTACCCGGCTCAG                         GTGTTGGCAAAACCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG
EST: gi|50324993|gb|CO520119.1|CO520119
EST:     GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTGGCAAAATCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG
EST: gi|74234865|gb|DT642779.1|DT642779
EST:     GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTGGCAAAATCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG
EST: gi|148953372|gb|EE152866.2|EE152866
EST:     GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTGGCAAAATCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG
EST: gi|211523327|gb|FL357648.1|FL357648
EST:     GCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCCGGCTCAG                         GTGTTGGCAAAATCTTCTAAGATGATTCCTG
genomic: GCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCC-GGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG
EST: gi|78107092|gb|DV525510.1|DV525510
EST:     GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTGGCAAAATCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG
EST: gi|71318369|gb|DR795946.1|DR795946
EST:     GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTGGCAAAATCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG
EST: gi|71440454|gb|DR821504.1|DR821504
EST:     GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAG                         GTGTTGGCAAAATCTTCTAAGATGATTCCTG
genomic: GGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG

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), 31 (downstream exon)
Score: 204

CAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG


Block sizes: 48 (upstream exon), 31 (downstream exon)
Score: 179

CAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 213

CAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG


Block sizes: 49 (upstream exon), 31 (downstream exon)
Score: 763

CAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttcc ... gtgtgaacagGTGTTGGCAAAATCTTCTAAGATGATTCCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCGCACCGATATGGAAGTACTGGGGCGTCAGCGTCACCAATACCATCGGGCCGACCATGGGGATCGAGGCTCTCAAGTACATCAGCTACCCGGCTCAGgtatggttccacctgttcttgctgtgtgactgtgtcgccttccttggttgttttacttttatgcactgtcccggagcggcggaaacgattaatgacaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgccttcc