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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttacccttctttctattattttttctctcttcatttggttatccctggtttgagattttacagaaaaaaaattatgtgctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGCGCAGGAGCTGGCAACGACACCACTGCCGCCGGCGTCCTTGCTGACATAA

Basic information

species Zea mays
transcript GRMZM2G151977_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151977_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g03190.1 (Oryza sativa), 3'ss of exon 11
--------gtaatgttacccttctttctattattttttctctcttcatttggttatccctggtttgagattttacagaaaaaaaattatgtgctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGCGCAGGAGCTGGCAACGACACCACTGCCGCCGGCGTCCTTGCTGACATAA
        |  | | |       | | |  ||| |  | | |     || |||  |   || | ||| |  | | ||  |      | ||| ||     ||||| ||||||||||||||||| ||| ||||| ||||||||||||| |||||||| ||||||||||| || |||||||| || || || |||||||||||| 
tctgttttgagaggattaaagaatgtttgatatgtgattttttactgtt-ggtagtgagtgatgtgaaacgtaaaagtgacgctgctttgttct-tgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGCGCTGGAGCTGGCAATGATACCACTGCAGCTGGAGTTCTTGCTGACATAC

upper sequence: GRMZM2G151977_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g03470.1 (Oryza sativa), 3'ss of exon 12
--------gtaatgttacccttctttctattattttttctctcttcatttggttatccctggtttgagattttacagaaaaaaaattatgtgctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGCGCAGGAGCTGGCAACGACACCACTGCCGCCGGCGTCCTTGCTGACATAA
        |  | | |       | | |  ||| |  | | |     || |||      || | ||| |  | | ||  |      | ||| ||     ||||| ||||||||||||||||| ||| ||||| ||||||||||||| |||||||| ||||||||||| || |||||||| || || || |||||||||||| 
tctgttttgagaggattaaagaatgtttgatatgtgattttttactgtt-ggtagagagtgatgtgaaacgtaaaagtgacgctgctttgttct-tgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGCGCTGGAGCTGGCAATGATACCACTGCAGCTGGAGTTCTTGCTGACATAC
















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|86473774|gb|DY240144.1|DY240144
EST:     AGCTCCCAAAGGATTTTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
genomic: AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|67018901|gb|CO447650.1|CO447650
EST:     AGTTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
genomic: AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|37373740|gb|CF623185.1|CF623185
EST:     AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
genomic: AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|101393898|gb|EB818882.1|EB818882
EST:     AGCTCCCAAAGGATTTTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCTTCTGGTGATCCAGGGC
genomic: AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|37391307|gb|CF632895.1|CF632895
EST:     AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGAGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
genomic: AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|67013499|gb|CO442248.1|CO442248
EST:     AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
genomic: AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|94478774|gb|EB707732.1|EB707732
EST:     AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
genomic: AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|5761968|gb|AI967016.1|AI967016
EST:     AGCTCCCAAAGGATTTTGCGCTGGGTAGATTGAGGGGAAGTGCCAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
genomic: AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|37386125|gb|CF630238.1|CF630238
EST:     AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
genomic: AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|18181178|gb|BM382388.1|BM382388
EST:     AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
genomic: AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|94478508|gb|EB707466.1|EB707466
EST:     GATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATTCAGGGC
genomic: GATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|31362355|gb|CD446712.1|CD446712
EST:     GGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTATCAGAGCTCCCTTCTGGTGATCCAGGGC
genomic: GGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|93016571|gb|EB642091.1|EB642091
EST:     AGCTCCCAAAGGATTTTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATTCAGGGC
genomic: AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|60349556|gb|DN216529.1|DN216529
EST:     AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
genomic: AGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
EST: gi|40334075|gb|CK368145.1|CK368145
EST:     GCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAAGTGACA-TGTG                         GTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC
genomic: GCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAA-GTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGC

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), 49 (downstream exon)
Score: 53

GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGCGCAGGAGCTGGCAACGACACCACTGCCGCCGGCGTCCTTGCTGACATAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 66

GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGCGCAGGAGCTGGCAACGACACCACTGCCGCCGGCGTCCTTGCTGACATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGCGCAGGAGCTGGCAACGACACCACTGCCGCCGGCGTCCTTGCTGACATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 78

GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttac ... ctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGCGCAGGAGCTGGCAACGACACCACTGCCGCCGGCGTCCTTGCTGACATAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggttatccctggtttgagattttacagaaaaaaaattatgtgctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGCGCAGGAGCTGGCAACGACACCACTGCCGCCGGCGTCCTTGCTGACATAA
               tttgagattttacaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgttacccttctttctattattttttctctcttcatttggttatccctggtttgagattttacagaaaaaaaattatgtgctgccatcagGTCGAGATATACAGCAGATGTTACCAGAGCTCCCCTCTGGTGATCCAGGGCGCAGGAGCTGGCAACGACACCACTGCCGCCGGCGTCCTTGCTGACATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT