Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattccttttgtagatgttatactttcagttgttcagtatagccatctagtttttccatatgccatctgtagtaccttacttttggttcatatttgttgacag

Basic information

species Zea mays
transcript GRMZM2G097226_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 11
GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattccttttgtagatgttatactttcagttgttcagt--atagc-catctagttttt---ccatatgccatctgtagtaccttacttttggttcatatttgttgacag
|| ||||| ||| ||||||| |||||||||||||||||||| ||  ||| | || |   | ||  ||||||     | |  |||   |||| |  ||||   ||| || |         | ||||| ||||   |  ||||||   | ||
GCCGCAGATATATTGTCCAAAGAAGGAATCAGTGCTGAGgtgatcacttgt-taaacaatttatgttcagtataataatctataatgcatcaatcttttcaaccacatactgcaaaagtttccttattttttactgctatttgccaatag

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 11
GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt---ttgtagatgttatactttcagttgttcagtatagccatctagtttttccatatgccatctgtagtacct-tacttttggttcatatttgttgacag
||||| |||| |||| | |||||||||||||||||||||||||  | ||   || ||       | |   |  || | ||  |    ||| | | || ||   |||     ||  || | | | |   | |                 
GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaactttagtttataatgaactttccccctcttttgcaaaaacttcatttgggttatcataatggtgagtgatgttcttatccgcatag-----------------

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA14G02380.1 (Glycine max), 5'ss of exon 11
GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattccttttgtagatgttatactttcagt-tgttcagtatagccatctagtttttccatatgccatctgtagtaccttacttttggttcatatttgttgacag
||||| |||| |||| | |||||||||||||||||||||||||  | ||| ||   |  |  |||| |  | | ||  | | |  ||||    |||    ||||  |   || |     | || ||  | || ||          
GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaac-tttagtttgtaatgaacttcccctcttttttgcaaaagcatca---tttgggttatgataatggt-gagtgatgctctta-tccacatag--------

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 11
GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattccttttgtagatgttatactttcagttgttcagtatagccatctagtttttccatatgccatctgtagtaccttac-ttttggttcatatttgttgacag
||||| |||| |||| | |||||||||||||||||||||||||  | ||  ||  ||  |  |||| |     ||   |  ||  |  |  |||     ||||  |   || ||   | |  || | || || |           
GCTGCTGAGACACTGGCAAAGGAAGGAATCAGTGCTGAGgtaaaacatta-gtttataatgaacttccccccttttt-tgcagaaacttcatttgggt-tatgata---gtggtgagtgatgttcttgtccacacag--------

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|32802035|gb|CD954271.1|CD954271
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCGATCAGACCACTTGATAGAGCTGCTATTA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTA
EST: gi|89754920|gb|DY685537.1|DY685537
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|78092463|gb|DV520837.1|DV520837
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|60394298|gb|DN227168.1|DN227168
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|211317947|gb|FL318710.1|FL318710
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|88757272|gb|DY541413.1|DY541413
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTACTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|76912074|gb|DV164558.1|DV164558
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|60343110|gb|DN210083.1|DN210083
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|211088145|gb|FL307530.1|FL307530
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAT                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|32829636|gb|CD969314.1|CD969314
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|86473456|gb|DY239826.1|DY239826
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|32829111|gb|CD968789.1|CD968789
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
EST: gi|211019433|gb|FL375798.1|FL375798
EST:     GCTGCAGAGATACTGTCCAAGGAAGGAATCAGCGCTGAG                         GTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA
genomic: GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCA

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: 39 (upstream exon), 49 (downstream exon)
Score: 181

GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 239

GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 238

GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 313

GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattcctt ... ttgttgacagGTGATCAACCTTCGATCAATCAGACCACTTGATAGAGCTGCTATTAATGCATCTGTCAGGAAAACCAACCGATTGGTGACTGTTGAAGAAGGGTTCCCCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGCAGAGATACTGTCCAAGGAAGGAATCAGTGCTGAGgtaattccttttgtagatgttatactttcagttgttcagtatagccatctagtttttccatatgccatctgtagtaccttacttttggttcatatttgttgacag

 CTGCAG
- - - - - - - - - AAGGAA
- - - - - - - - - - - AAGGAA