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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtcctttattttagcatgttattctatatatgtttttttgagacatttggttatgtaccccacaagaatatcttagttattctttttgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG

Basic information

species Zea mays
transcript GRMZM2G458208_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 7
gtaagtgtcctttattttagcatgttattctatatatgttttt--ttgagacatttggttatgtaccccacaagaatatcttagttattct-ttttgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG
                   | | ||| ||  |  | |||| ||  |||| |  ||  ||| |    |       | ||||| ||| ||    || |   | ||||||| |||| ||||| |||||| | || ||||||||||||||| ||||| ||||||| || ||||| || || ||  |||||||||||
-------------------gtaagtt-tttaacttctgttgttggttgatatgttcagtttt---tcttttggaactatctaagtcatgaggttatatttaacagGAACTGGATGACCCCTTGATCCTGATACATGACAAGAAGGTTTCGAACCTGCATGCAGTAGTTAAAGTCTTGGAGTTGGCTCTGAAG
















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|33094209|gb|CF054203.1|CF054203
EST:     GTACTTCATTACCAACCCAAAAACCCAGAAATGT                         GAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
genomic: GTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
EST: gi|31357599|gb|CD441956.1|CD441956
EST:     GAGGCTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGT                         GAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
EST: gi|61119163|gb|DN560124.1|DN560124
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACCCAAAAACCCAGAAATGT                         GAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
EST: gi|13388799|gb|BG462407.1|BG462407
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGT                         GAATTGGAAGACCCATTGATCTTAATTCATGACAAGAA
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAA
EST: gi|31361464|gb|CD445821.1|CD445821
EST:     GAGGCTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGT                         GAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
EST: gi|88747169|gb|DY531310.1|DY531310
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGT                         GAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
EST: gi|5499101|gb|AI854968.1|AI854968
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACCCAAAAACCCAGAAATGT                         GAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
EST: gi|31349389|gb|CD433746.1|CD433746
EST:     GAGGCTACATCTCTCCGTACTTCATTAC-AACTCAAAAACCCAGAAATGT                         GAATTGGAAGAACCATTGATCTTAATTCATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATG
EST: gi|67016113|gb|CO444862.1|CO444862
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGT                         GAATTGGAAGACCCATTAATCTTAATTCATGACAAGAAGGTTACGAACATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
EST: gi|94476466|gb|EB705424.1|EB705424
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGT                         GAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG
EST: gi|67023196|gb|CO451945.1|CO451945
EST:     GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGT                         GAATTGGAAGACCCATTAATCTTAATTCATGACAAGAAGGTTACGAACATG
genomic: GAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATG

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: 761

TAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 514

TAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 306

TAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 786

TAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGAAATGTgtaagtgtcc ... tgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacatttggttatgtaccccacaagaatatcttagttattctttttgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG
                                   ttattctttttgcctc  CT-rich tract
                         aatatcttagttattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtcctttattttagcatgttattctatatatgtttttttgagacatttggttatgtaccccacaagaatatcttagttattctttttgcctcacagGAATTGGAAGACCCATTGATCTTAATTCATGACAAGAAGGTTACGAACATGCATGCTGTGGTTAAGGTTTTAGAAATGGCTCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG