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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctgaaacctggttacatttcaaaccttatccttgctgtaatgctaattttccttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG

Basic information

species Zea mays
transcript GRMZM2G178102_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g41860.1 (Oryza sativa), 3'ss of exon 3
gtaagcctgaaacctggttacatttcaaaccttat---------ccttgctgtaatgctaatt----------ttccttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG
|||  |   |||||||||    ||||     || |         | ||  ||||      |||          ||   ||||  |||||| |||||||||||||||||||| ||||||||||||||||| |||||||| |||||||||||| | ||||||||||||||||||||||||
gtatccacaaaacctggtctattttcttcttttgttaggccgtgcttttttgtatgaaagattgctgagatgattttatttgcgcagTCTTCTCGCTATTGCTGAGGAGACCTTGGCAGAGTTCATGTCGAAGGCGACAGGAACTGCTGTCGAATGGGTGCAAATGGTTGGGATGAAG

upper sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G13640.1 (Glycine max), 3'ss of exon 3
-------------------gtaa-gcctgaaacctggttacatttca----aaccttatccttgctgtaatgcta--attttcc--ttttgtc-cagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG
                    |||  | |    | |  |||  |||||    ||  || || | |   |||| | |  ||| | |  ||||||  |||||| ||||| || |||||||||||  ||||||||||| | |||||||| ||||||||||||||| ||||||| || ||| |||||||||||
gtaagtaacattacataacataacacgtacttctttattatttttcatttcaatgttttcatggtaataataccatcattgttcatttttgtttcagTCTTCTCGCCATAGCTGAGGAGACCCTGGCAGAGTTCCTTTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG

upper sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 3
----gtaagcctgaaac-ctggttacatttcaaaccttatccttgctgtaatgctaattttccttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG
    ||||  |    |  |     | |||    |  | ||   ||||      | | | ||  || || ||||||| || || |||||| |||||||  |||| | |||| | || || || ||||||||||||||||||||||| |||||| |||||||||||
gtaagtaactccattatgcaaacaaaattgtttaattaatatatgctcattcaccattctttattctg-ccagTCTTCTTGCAATTGCTCAGGAGACCCTGGCGGCGTTCCTTTCAAAAGCTACTGGAACTGCTGTCAACTGGGTCCAAATGATTGGGATGAAG

upper sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G30000.1 (Glycine max), 3'ss of exon 3
---------------------gtaagcctgaaacctggttacat-ttcaaaccttatccttgctgtaatgctaattttccttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG
                       ||   ||     |   || ||  |||  |   ||| || | |     |||||| |   ||   ||||||| || ||||||||| |||||||  | |  |||||| | ||||| || ||||||||||||||||||||||| || ||| |||||||||||
gtaagtaacttcattatgcaaacaaatttgtttaattaatatatactcattcaccatcattac-gggtctctaattctttattctgccagTCTTCTTGCTATTGCTCAGGAGACCCTAGTGGAGTTCCTTTCCAAAGCTACTGGAACTGCTGTCAACTGGGTCCAGATGATTGGGATGAAG

upper sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G02750.1 (Glycine max), 3'ss of exon 3
-------------------------gtaagcctgaaacctggttacatt--tcaaaccttatccttgctgtaa----tgctaattttccttttgtc-cagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG
                         |||   |  |||  |   ||  ||  |||     ||    |    |||    ||   ||| |   |||||  |||||| ||||| || |||||||||||  ||||||||||| | |||||||| ||||||||||||||| ||||||| || ||| |||||||||||
taacaaaaactaacaattaacatttgtagatccaaaaaataaatattttcatcagtaaatagtaataacataaggattgtggattatttgtttgtttcagTCTTCTCGCCATAGCTGAGGAGACCCTGGCAGAGTTCCTTTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG

upper sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------gtaagcctgaaacctggttac--atttcaaaccttatccttgctgtaatgctaat--tttccttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG
             ||  ||   | | ||   ||   | |||         |  ||    ||    |||  ||   ||||||  || || ||  |||| || |||||| |  | ||||||||| | |||||||| || |||||||||||  ||||||| || ||| |||||||||||
gtgagcttttcttgtctgctctataactctctaatgaattctgtttcccactctgtgacaacctaaatggttcttttttgtttagACTCCTTTCTATAGCAGAGGAGGCCCTAGCAGAGTTCCTTTCCAAGGCTACAGGAACTGCTGTTGACTGGGTTCAGATGATTGGGATGAAG

upper sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 3
-----gtaagcctgaaacctggttac--atttcaaaccttatccttgctgtaatg--ctaatt----ttccttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG
     | | ||        || ||    |||||  |   |  | ||     ||    |||| |    |   ||||    ||||| ||| | ||||| |||||||| ||||| |||||| | | |||||| || |||||||||||| ||||||| || ||| |||||||||||
gtaaggaaggctctttttttgtttgtgaatttctcattgtgacattatgagaagagactaaatggagtgtttttttggtagTCTTCTCTCGATTGCGGAGGAGACCTTGGCGGAGTTCCTTTGCAAGGCTACAGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG

upper sequence: GRMZM2G178102_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 3
------------------gtaagcctgaaacctggttacatttcaaaccttatccttgctgta-atgct----aattttccttt---tgtc-cagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG
                   | |  |||| |    |  | ||  | ||  |  |  ||| | || |||||    |   ||| |||   ||||  ||||||||||| || |||||||||||  ||||||||||| |||||||||| ||||||||||||||| ||||||| || ||| |||||||||||
gtaacttactttcaactatttaatctgatataaaga-aaatacctaatttcctggttgatttacatgcttacgagccttcttttgtgtgtcatagTCTACTCGCAATAGCTGAGGAGACCCTGGCAGAGTTCCTGTCCAAGGCTACTGGAACTGCTGTCGACTGGGTCCAGATGATTGGGATGAAG

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|149071186|gb|EE159583.2|EE159583
EST:     AACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGG                         TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGAC
genomic: AACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGGgtaagcctga ... ttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGAC
EST: gi|89247876|gb|DY619662.1|DY619662
EST:     AACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGG                         TCTACTCGCTATTGCTGAGGAGACATTGGCAAAGTTCATGTCCAA
genomic: AACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGGgtaagcctga ... ttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAA
EST: gi|148960630|gb|EE011258.2|EE011258
EST:     AACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGG                         TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGAC
genomic: AACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGGgtaagcctga ... ttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGAC
EST: gi|149110140|gb|EE293958.2|EE293958
EST:     AACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGG                         TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGAC
genomic: AACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGGgtaagcctga ... ttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGAC
EST: gi|148999153|gb|EE036067.2|EE036067
EST:     AACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGG                         TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGAC
genomic: AACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGGgtaagcctga ... ttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGAC
EST: gi|148972955|gb|EE023980.2|EE023980
EST:     AACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGG                         TCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGAC
genomic: AACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGGgtaagcctga ... ttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGAC

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: 88

ACACAAGCTGTGAGTCTGTGGTGACAAGTGGTCAGCACAACCAACAGCAAAACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGGgtaagcctga ... ttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 15

ACACAAGCTGTGAGTCTGTGGTGACAAGTGGTCAGCACAACCAACAGCAAAACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGGgtaagcctga ... ttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 47

ACACAAGCTGTGAGTCTGTGGTGACAAGTGGTCAGCACAACCAACAGCAAAACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGGgtaagcctga ... ttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 17

ACACAAGCTGTGAGTCTGTGGTGACAAGTGGTCAGCACAACCAACAGCAAAACCCAGCAGTTCTGCATCCTCCACAAAGGGATGCGAACAACCCAGCAGGgtaagcctga ... ttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggttacatttcaaaccttatccttgctgtaatgctaattttccttttgtccagTCTACTCGCTATTGCTGAGGAGACATTGGCAGAGTTCATGTCCAAGGCGACTGGAACTGCTGTCAACTGGGTGCAAATGGTTGGGATGAAG
                                 tgctaat  putative branch site (score: 17)
                                       ttttccttttgtcc  CT-rich tract
                                    taatttt  TA-rich tract