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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaaatttgagattgtaactgatgaactagtgaatccaaattagtatagacatgtcgctattgatactaagctcttatgtttcccttcagttaa...

Basic information

species Zea mays
transcript GRMZM2G109624_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109624_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 5'ss of exon 11
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaaatttgagattgtaactgatgaactagtga---atccaaattagtat-agacatgtcgctattgatactaagctcttatgtttcccttcagttaa
|||||||||||||||||||||||||||||||||||||| ||||||||| | || |||||||| |||||  |||| ||||| |||||||||  ||  |||   |||   |   | ||||| | |   | ||| ||  |||| ||     ||   ||    || |   ||| || || | | | ||    
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTTGTGTCAAGGTTGCTGCAGTACTCGCCAAATTTGCGTTGCACAGCTgtaagactaatattggatttgagccattttaactaattattgaaccagatcggtattaggtggatcatcatgagcacaataatctaat-ttcctcataaga---

upper sequence: GRMZM2G109624_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA07G08320.1 (Glycine max), 5'ss of exon 11
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaaatttgagattgtaactgatgaactagtgaatccaaattagtatagacatgtcgctattgatactaagctcttatgtttccct--tcagttaa--
 |||||   ||| | ||||| |||||||| || ||||| ||||||||||| || || || |||||||| || || ||||| ||||||||     |||||   ||| || || | | ||| |  ||| | ||||    | |||| |  | ||  |     || | || | |   | |  |||   ||  
GTTTTTCACAAGAGAATGCCGCCTGAAGCCGTGGATCTTGTGTCAAGGCTGCTGCAATATTCACCAAATCTACGTTGCACCGCTgtaag--ttgatttgctcttgaaaatg-ttacctattatatctagattaaataatacatatt-caatcaaactacagtttttgtatacacatactcaccaaaga

upper sequence: GRMZM2G109624_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA18G45960.1 (Glycine max), 5'ss of exon 11
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaaga-acaaatttgagattgtaactgatgaacta-gtgaatccaaattagtatagacatgtcgctattgatactaagctcttatgtttcccttcagttaa
 |||||   |||   |||||  | ||||| || ||||| ||||||||| | |||||||| |||||||| || || ||||||||||||||     ||||||    |  || || ||   |  || |    || |  ||||  |  |  | ||| |||   |   |  |  |    |      ||   
-TTTTTCACAAGAAGATGCCTTCAGAAGCAGTGGATCTAGTGTCAAGGATGCTTCAGTATTCACCAAATCTACGATGCACTGCTGtaagttgttaatttgcttctagaaatgttgccttttgttagcttaattgtgtattca-gtcacactaatgaagatggaccatctttacacatgatggtatt

upper sequence: GRMZM2G109624_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA03G01850.1 (Glycine max), 5'ss of exon 11
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaaatttgagattgtaactgatgaactagtgaatccaaattagtatagac-atgtcgctattgatactaagctcttatgtttcccttcagttaa
 |||||   ||| | ||||||||||||||||| ||||| || |||||||| ||||| || |||||||| || || ||||||||||||||   |  ||||| | ||| ||  || |  |   || | || | ||  |||    ||    |||  | |  ||    |  ||  || ||       ||
GTTTTTCACAAGAGAATGCCACCTGAAGCTGTGGATCTTGTATCAAGGCTGCTTCAATATTCACCAAATCTACGTTGCACTGCTgtaagttgatttttgaaaatgttacctattatatctagattacataata-catatttgatcaaactacagtttttatatgcacatacttaccaaagaagaa

upper sequence: GRMZM2G109624_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA09G40150.1 (Glycine max), 5'ss of exon 11
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaaattt-------gagat---------tgtaactgatgaactagtgaatccaaattagtatagacatgt-cgct-----attgatactaagctct---tatgtttcccttcagttaa-------------------------------------------------------------------------
 |||||   |||   |||||  | ||||| || ||||| ||||||||| | |||||||| ||||| || || || ||||||||||||||    |||||       || ||         |||| || |   |    || |  || | || |  |||  | |  | |     | | ||||| |||| |    ||||||  | |   || |                                                                         
GTTTTTCACAAGAAGATGCCTTCAGAAGCAGTGGATCTAGTGTCAAGGATGCTTCAGTATTCACCGAATCTACGATGCACTGCTgtaagttttaattttcttctagaaatgtcaccttttgtagcttaattatatatgcagtcacactaatgaagatttatatgttgaaaaaattatacttagctttatccatgttttacatagtttcatattatagaagttaggaagatattcaattttctttggttattctgttgtgctaatgattattttctgttgcag

upper sequence: GRMZM2G109624_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 5'ss of exon 11
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaaatttgagattgtaactgatgaactagtgaatcca---aattagtatagacatgtcgctattga----tactaagctcttatgtttcccttcagttaa-
 ||||    ||||| |||||||||||||| || || ||||| ||||| || |||||||||||||||||||| || |||||||| ||||||  ||||    | | |  ||     |||||   ||||        |  | | ||  | ||    |  |    ||| || | |||   ||| || |  ||||| 
ATTTTCCACAAGCGAATGCCACCTGAAGCAGTAGACCTCGTCTCAAGACTCCTTCAGTACTCACCAAACCTTCGTTGCACTGCAgtaagactaaatcct-gctggacaccacaaaactatataatctccttggctgatttggaattttctaactcaaattctacaaaacacttt--ttttccatttgttaag

upper sequence: GRMZM2G109624_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S306_43V6.2 (Physcomitrella patens), 5'ss of exon 10
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaaatttgagat-tgtaactgatgaactagtgaatccaaattagtatagacatgtcgctattgatactaagctcttatgtttcccttcagttaa-
 ||||    || ||||||||||||||||| |||||  | ||||||||||| ||||||||||| ||||| ||||| ||||  ||||| || |      |    | |||   || |      ||||     |  | || | |   ||     | |  |      ||   | ||  ||    ||  |  
GTTTTCCACAAACGCATGCCACCTGAAGCAGTTGACTTGGTGTCAAGGCTCCTTCAGTACTCTCCAAATCTGCGGTGCAACGCTgtgagtagcgtcatattctgtgttgttggtacgggtgtgatgttgagct-gtgtgggtctgcgttgagtcgtggcgttctgcgaggtg-ccaacgaggcatt

upper sequence: GRMZM2G109624_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 5'ss of exon 9
CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaaatttgagattgtaactgatgaactagtgaatccaaattagtatagacatgtcgctattgatactaagctcttatgtttcccttcagttaa---
 ||||    ||||||||||| || ||||| || ||||| || |||||||||||||||||||| || || ||||| |||| |||||| ||   |     | | || |   |  |||| |  |||   |  |  |  || |    ||  | ||  ||  |   ||||  || |        | |     
GTTTTCCACAAGCGCATGCCTCCAGAAGCAGTAGATCTGGTTTCAAGGCTACTTCAGTACTCTCCGAATCTGCGGTGCAATGCTgtgagtg-atgacggggtttttctgttgtgaagtgttgatcgcgcag-accatcgttg-gttacgatgaatctttctctctattggtgggaacaggatgttga

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|213179091|gb|FM180755.1|FM180755
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|60399462|gb|DN232274.1|DN232274
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|31664051|gb|CD573231.1|CD573231
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCGCTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|32944815|gb|CF049634.1|CF049634
EST:     GTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: GTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|5607686|gb|AI901353.1|AI901353
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|116824778|gb|EC868424.1|EC868424
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|12973361|gb|BG268442.1|BG268442
EST:     TCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: TCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|60354737|gb|DN221710.1|DN221710
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|60338924|gb|DN205897.1|DN205897
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|21626337|gb|BQ621258.1|BQ621258
EST:     ATCTCGTGTCAAGCCTACTTCAGTACTCACCAAACCTGCGCTGCCCTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
EST: gi|78025807|gb|DV494194.1|DV494194
EST:     ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCT                         GTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC
genomic: ATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTC

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: 882

CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 202

CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 175

CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 222

CTTTTTGGTAAGCGCATGCCACCTGAAGCTGTTGATCTCGTGTCAAGGCTACTTCAGTACTCACCAAACCTGCGCTGCACTGCTgtaagaacaa ... atattttcagGTTGATGCTTGTGCCCATCCATTCTTTGATGAGCTGCGGGACCCCAAGGTCTGCTTGCCAAGTGGACGACCGCTGCCAGCGCTGTTCGACTTCACAGCAG