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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatctcaaagctatttagcttcttaactgttgttttattttatgttattgctaatttggtaaagacatatttggttcgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCTGGTCGGTCTAACAGTTTTGAGTCTAGTAAACAATGCACTATAAAGCATG

Basic information

species Zea mays
transcript GRMZM2G114861_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g53760.1 (Oryza sativa), 3'ss of exon 11
gttagtatct-caaagctatttagcttcttaactgt-tgttttattttatgttattgctaatttggtaaagacatatttggttcgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCTGGTCGGTCTAACAGTTTTGA---GTCTA---GTAAACAATGCACTATAAAGCATG
|||||||||   |  || ||  || |||| || |||   || ||| |  ||||  ||  | |||                 | |  |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| |  |||||   |||||   ||||||||| ||| ||||      
gttagtatccatagtgcaatgcagattctgaagtgtacattctatgtagtgttgctgagagtttt----------------tcctatgtgcagGCATCAATGTTGGAAATATACAATGAGACAATTCGTGATTTGTTAGCACCTGGTCGGTCTAATAACTTTGATCTGTCTACCAGTAAACAATACACCATAA------

upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA13G36230.2 (Glycine max), 3'ss of exon 12
gttagtatctcaaagctatttagcttcttaactgttgttt-tattttatgttattgctaatttggtaaagacatatttggttcgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCTGGTCGGTC--TAACAGTTTTGAGTCTAGTAAACAATGCACTATAAAGCATG
    ||     | || ||| |   |  |||      | |  ||  || || | |||     |  | |||      ||        |   ||||  || |||||||||||||||||||| |||||||||||| |||||||  |   |  |||   | ||| |   |  | |  |     || |  ||    |   
----gtgaagtagag-tatattcttcgttattcacagatcataaattttgatgttgaggtctaagaaaattttccttcttcaaaattaacagGTGTCTATGTTGGAAATATACAATGAAACCATTCGTGATCTGTTAGCTACAAATAAGTCATCAGCAGATGGAACACCAACACGTG-TGGAAAATGGTACTC-

upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA12G34330.1 (Glycine max), 3'ss of exon 11
gttagtatctcaaagctatttagcttcttaactgttgttttattttatgttattgctaatttggtaaagacatatttggttcgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCTGGTCGGTC--TAACAGTTTTGAGTCTAGTAAACAATGCACTATAAAGCATG
    ||     | ||| ||||   |  ||   |      | |||  |   | |    | |||    | ||    ||       ||   ||||  ||||||||||||||||||||||| |||||||||||| ||||| |  |   |  |||   | |||     |  | |  |   | || |  ||    |   
----gtgatatagagc-atttccttctttttttcacacatgattgcaatgtttataaattttaaggatgattcgttcataaaatttaacagGTGTCAATGTTGGAAATATACAATGAAACCATTCGTGATCTGTTATCTACAAATAAGTCATCATCAGAAGGAACACCAACACG-AGTGGAAAATGGTACTC-

upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 11
-------gttagtatctcaaagctatttagcttcttaactgttgttttattttatgttattgctaa---tttggtaaagacatatttggttcgttg-------tgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCTGGTCGGTCTAACAGTTTTGAGTCTAGTAAACAATGCACTATAAAGCATG--
          | |||      ||  ||| | |  ||  ||| |      ||  |||||||  |||      | || || |||| | |  |||   |       || |||  ||||||||||||||||| ||||| || ||||||||||||||| || |   ||| ||   |  | |   ||||    ||||    |   |   ||  |  
gtgagcaagcaatattatcttgcctttttgttcattttctgcttaccctttgaatgttatgtctatggtcattgtgaacacatgtcttattctaagatatatttgtagGTTTCAATGTTGGAAATATATAATGAAACAATTCGTGATTTGTTATCAACAAATCGATCCTGC--TCTGATGTCTCACGAACAGAAAATGGTGTTGCTGGAA

upper sequence: GRMZM2G114861_T01 (Zea mays), 3'ss of exon 11
lower sequence: PP1S87_179V6.1 (Physcomitrella patens), 3'ss of exon 11
gttagtatctcaaagctatttagcttc-ttaactgttgtttt--attttatgttattgctaatttggtaaagacatatttggttcgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCTGGTCGGTCTAACAGTTTTGAGTCTAGTAAACAATGCACTATAAAGCATG---
           |    ||  |     | |||||  | ||||   |   |  |||   |   |||   |||   |  |    |  |    |||||||||||||||| ||||| ||||| || ||||||||||||||| | ||    || |     ||  |   ||  || || |||   |      | |||||||   
---------gtacgattacatgctgccattaaccttcgtttagaagggtgggttggagaacattaactaattgcgaagcatgg-caccttgcagGCATCAATGTTAGAAATCTACAACGAAACCATTCGTGATTTGCTGGCGAAAGGGCCAGTGAATGGAGATG--TCAAGCAAATG-TATGTGGTGAAGCATGACC

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|67019346|gb|CO448095.1|CO448095
EST:     TCAAGACCAGTCGGTTTCTAGAATCTCAAGGATGGAATTATTCCATGCAA                         GCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCT
genomic: TCAAGACCAGTCGGTTTCTAGAATCTCAAGGATGGAATTATTCCATGCAAgttagtatct ... cgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCT
EST: gi|87155658|gb|DY400447.1|DY400447
EST:     TCAAGACCAGTCGGTTTCTAGAATCTCAAGGATGGAATTATTCCATGCAA                         GCATCAATGTTGGAAATATACAATGAGACCATTC
genomic: TCAAGACCAGTCGGTTTCTAGAATCTCAAGGATGGAATTATTCCATGCAAgttagtatct ... cgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTC
EST: gi|67014413|gb|CO443162.1|CO443162
EST:     TCAAGACCAGTCGGTTTCTAGAATCTCAAGGATGGAATTATTCCATGCAA                         GCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCT
genomic: TCAAGACCAGTCGGTTTCTAGAATCTCAAGGATGGAATTATTCCATGCAAgttagtatct ... cgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCT
EST: gi|78085386|gb|DV513779.1|DV513779
EST:     TCAAGACCAGTCGGTTTCTAGAATCTCAAGGATGGAATTATTCCATGCAA                         GCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCT
genomic: TCAAGACCAGTCGGTTTCTAGAATCTCAAGGATGGAATTATTCCATGCAAgttagtatct ... cgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCT

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), 48 (downstream exon)
Score: 159

ACCAGGAAATGATCAAAAAGGGATAATACCTCGTTCTTTGGAGCAAATTTTCAAGACCAGTCGGTTTCTAGAATCTCAAGGATGGAATTATTCCATGCAAgttagtatct ... cgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCTGGTCGGTCTAACAGTTTTGAGTCTAGTAAACAATGCACTATAAAGCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 41

ACCAGGAAATGATCAAAAAGGGATAATACCTCGTTCTTTGGAGCAAATTTTCAAGACCAGTCGGTTTCTAGAATCTCAAGGATGGAATTATTCCATGCAAgttagtatct ... cgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCTGGTCGGTCTAACAGTTTTGAGTCTAGTAAACAATGCACTATAAAGCATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 38

ACCAGGAAATGATCAAAAAGGGATAATACCTCGTTCTTTGGAGCAAATTTTCAAGACCAGTCGGTTTCTAGAATCTCAAGGATGGAATTATTCCATGCAAgttagtatct ... cgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCTGGTCGGTCTAACAGTTTTGAGTCTAGTAAACAATGCACTATAAAGCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 226

ACCAGGAAATGATCAAAAAGGGATAATACCTCGTTCTTTGGAGCAAATTTTCAAGACCAGTCGGTTTCTAGAATCTCAAGGATGGAATTATTCCATGCAAgttagtatct ... cgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCTGGTCGGTCTAACAGTTTTGAGTCTAGTAAACAATGCACTATAAAGCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttattttatgttattgctaatttggtaaagacatatttggttcgttgtgcagGCATCAATGTTGGAAATATACAATGAGACCATTCGTGATTTGTTAGCACCTGGTCGGTCTAACAGTTTTGAGTCTAGTAAACAATGCACTATAAAGCATG
                 tgctaat  putative branch site (score: 226)
     attttatgttattgct  TA-rich tract