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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccataaccacccaaaatccttaatggtagttctcaaagttcttgcgatcttcagttacaggcattcggtaataaatactttgtaatcattgtaaactttacaatgtcctttgatag

Basic information

species Zea mays
transcript GRMZM2G057408_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057408_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g45840.1 (Oryza sativa), 5'ss of exon 2
TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgta--atccataaccacccaaaatccttaatggtagttctcaaagttct-tgcgatcttcagttacaggcattcggtaataaatactttgtaatcattgtaaactttacaatgtcctttgatag
 || |||||||||||||| || ||||||||||| ||||||||||| ||||| |||||||||   | |||| | |||     |    | |    ||| |||   |||| ||| | | |   ||  ||      | | ||   |  |||| |  | || || |  |  |               
GTTCGATCGTGATTGGAAAAAGATTGAAGCATACGTTGGCTCAAAAACTGTGATACAGgtatggttcatagctacc-----tttcaagttaacgttttcattcttctctgctagcct---ttggagtggcgtgttgatgtttgatttg-aggcgttctatatgtatc---------------

upper sequence: GRMZM2G057408_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G24400.1 (Glycine max), 5'ss of exon 2
TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccataaccacccaaaatccttaatggtagttctcaaagttcttg-cgatcttcagttacaggca-ttcggtaataaatactttgtaatcattgtaaactttacaatgtcctttgatag
 ||||| ||||| ||||| || |||||||||| |||||| ||||||| ||||||||||||||| |  |   | | ||||  |||  |     | |   |||| |      ||||| |||      || ||      || ||| ||  |  | | | |   | |                  
GTTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGTTATACAGgtaattctaattgaacaaaaaaactttctt----tgcctgaagtgcagaattatctttagtatttctcaatttaagtctagatatttcatt-ttagtctgctcct------------------

upper sequence: GRMZM2G057408_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA16G29740.1 (Glycine max), 5'ss of exon 2
TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccataaccacccaaaa----tccttaatggtagttctcaaagttcttgcgatcttcagttacaggcattcggtaataaatactttgtaatcattgtaaactttacaatgtcctttgatag
 ||||||||||||||||| || |||||||||| |||||| ||||||| ||||||||||||||| |  |   | | ||||    | |||      |  | |  || |   |   |||||     |   |  |   |  ||    || | | ||  ||                           
GTTTGATCGTGATTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGAGTGTTATACAGgtaattctcattgaacaaaaaaactttctttgcctgaagtgtagaattatctttaatctttctcaatttgagtctag--atctgcacctagaaagtatccat-----------------------

upper sequence: GRMZM2G057408_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv16s0050g01180.t01 (Vitis vinifera), 5'ss of exon 2
TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccataaccacccaaaatccttaatggtagttctcaaagttcttgcgatcttcagttacaggcattcggtaataaatactttgtaatcattgtaaactttacaatgtcctttgatag
|||||| ||||||||||| || ||||| |||| |||||| |||||||| ||||| |||||||||   |       |  ||||||  |  |||     |  |  | | |       ||  | |   | |   |||| |    |||| |                                
TTTTGACCGTGATTGGAAAAAGATTGAGGCATTTGTTGGATCAAAGACAGTTATTCAGgtaatcaggattgtataattatcctt--ttatagact--atggcacataccccaagaagaaaaataaact---taatgatgcttttgcag-------------------------------

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|71448760|gb|DR829810.1|DR829810
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|101392321|gb|EB818090.1|EB818090
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|211503271|gb|FL119712.1|FL119712
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|91876492|gb|EB406449.1|EB406449
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|211500941|gb|FL119710.1|FL119710
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|211503273|gb|FL119714.1|FL119714
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|50336085|gb|CO531211.1|CO531211
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|211503279|gb|FL119720.1|FL119720
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAA-TACCTTTCCTGAAGGTTCAGAAGAAATGGT
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTAC-TT-CCTGAAGGTTCAGAAGAA-TGGT
EST: gi|211503277|gb|FL119718.1|FL119718
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCGATGCACAGAAG-ACCTTCCTGAAGGTTCAGAAGGAATGGTA
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTAC-TTCCTGAAGGTTCAGAAG-AATGGTA
EST: gi|89755460|gb|DY685870.1|DY685870
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|78118283|gb|DV536669.1|DV536669
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|89757689|gb|DY687184.1|DY687184
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|78076508|gb|DV504942.1|DV504942
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|211503280|gb|FL119721.1|FL119721
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|211500936|gb|FL119705.1|FL119705
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAG
EST: gi|148963456|gb|EE014475.2|EE014475
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCACAGACTGTTATACAG                         ATAAGGAGCCATG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATG
EST: gi|148956892|gb|EC902815.2|EC902815
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|71441161|gb|DR822211.1|DR822211
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|71428977|gb|DR810027.1|DR810027
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACG
EST: gi|211503278|gb|FL119719.1|FL119719
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATCAGGAGCCAT
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCAT
EST: gi|211500940|gb|FL119709.1|FL119709
EST:     GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAG                         ATAAGGAGCCATGCACAGAAG-ACTTTCCTGAAGGTTCAGAAGGAATGGTA
genomic: GTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTT-CCTGAAGGTTCAGAAG-AATGGTA

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: 93

TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACGGGCGAGCATCTGCCCCCACCCAGGCCAAAACGAAAGGCAGCTCATCCAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 82

TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACGGGCGAGCATCTGCCCCCACCCAGGCCAAAACGAAAGGCAGCTCATCCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 100

TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACGGGCGAGCATCTGCCCCCACCCAGGCCAAAACGAAAGGCAGCTCATCCAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 66

TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccata ... cctttgatagATAAGGAGCCATGCACAGAAGTACTTCCTGAAGGTTCAGAAGAATGGTACGGGCGAGCATCTGCCCCCACCCAGGCCAAAACGAAAGGCAGCTCATCCAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGATCGTGATTGGAAGAAAATTGAAGCATATGTTGGCTCAAAGACTGTTATACAGgtaatccataaccacccaaaatccttaatggtagttctcaaagttcttgcgatcttcagttacaggcattcggtaataaatactttgtaatcattgtaaactttacaatgtcctttgatag

- - - - - -  TGGAAG
- - - - - - - GGAAGA
- - - - - - - - AAGAAA
- - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - TGAAGC