Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtcactgtcagcgataggttccttcgcttgttctccttgtccatgtctcaatgactaacacagctgctgcctgcttcaatgtcccttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTCCATGAGCAAGGACCCCGTGGCTTGTTCAGGGGATGGATGGCCACACTGG

Basic information

species Zea mays
transcript GRMZM2G118208_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118208_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g15690.1 (Oryza sativa), 3'ss of exon 1
---------------------------gtccgtcactgtcagcgataggttccttcgcttgttctccttgtcca-tgtctcaatgactaacacagctgctgcctgcttcaatgtcccttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTCCATGAGCAAGGACCCCGTGGCTTGTTCAGGGGATGGATGGCCACACTGG
                            ||  |  || ||  | ||   |       ||  | |   |       |  || ||||  |||   |  |  ||  | |   |||||    |  |  |||| || ||| | ||||||||||||||| ||||||  ||||||||| ||||||| |||||||| |   |||| || |||| ||| ||||||||||| ||||
gtctttcgccgtgttactgtagctcaaatctctagct-tccccaatgactaatggaactcatacaaatcactagctccctaaatggttaatggaattcgtgtgtac---aatgtattcttgc--agGTTGACCCTGGTAAGTACAGGGACATTTCATCTGGATTTGGTGTCCTGCTCCAAGAGCAAGGTCTTGGTGGATTCTTCAAGGGCTGGATGGCCACGCTGG
















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|71438084|gb|DR819134.1|DR819134
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|78111853|gb|DV530250.1|DV530250
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|94478271|gb|EB707229.1|EB707229
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCA
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCA
EST: gi|26455981|gb|CA827564.1|CA827564
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|148979348|gb|EE026622.2|EE026622
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|101382650|gb|EB813379.1|EB813379
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|19770204|gb|BQ034925.1|BQ034925
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGGGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|211272280|gb|FL097587.1|FL097587
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|211272277|gb|FL097584.1|FL097584
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|211272278|gb|FL097585.1|FL097585
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|76281617|gb|DV021185.1|DV021185
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|211139874|gb|FL097576.1|FL097576
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|71417466|gb|DR804064.1|DR804064
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|211139873|gb|FL097575.1|FL097575
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|211272272|gb|FL097579.1|FL097579
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|211272274|gb|FL097581.1|FL097581
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|74245909|gb|DT653823.1|DT653823
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|71767406|gb|DR965343.1|DR965343
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|91874483|gb|EB404440.1|EB404440
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|211139876|gb|FL097578.1|FL097578
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|149078806|gb|EE167615.2|EE167615
EST:     CACTCACCTCGCTGTAACGCCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTTGGTGTCATGCT
genomic: CACTCACCTCGCTGTAACGCC-GCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTT-GGTGTCATGCT
EST: gi|94477100|gb|EB706058.1|EB706058
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|71426616|gb|DR807666.1|DR807666
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         ATGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|67010579|gb|CO439328.1|CO439328
EST:     CCTCGCTGTTACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: CCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|78078254|gb|DV506669.1|DV506669
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
EST: gi|93014922|gb|EB640442.1|EB640442
EST:     TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAG                         GTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC
genomic: TCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTC

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: 47 (upstream exon), 46 (downstream exon)
Score: 27

GCCGCTGTTCTACGCTACCTGCGCCCTCGGCGGCGTTCTCAGCACCGGCCTCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTCCATGAGCAAGGACCCCGTGGCTTGTTCAGGGGATGGATGGCCACACTGG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 13

GCCGCTGTTCTACGCTACCTGCGCCCTCGGCGGCGTTCTCAGCACCGGCCTCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTCCATGAGCAAGGACCCCGTGGCTTGTTCAGGGGATGGATGGCCACACTGG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 27

GCCGCTGTTCTACGCTACCTGCGCCCTCGGCGGCGTTCTCAGCACCGGCCTCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTCCATGAGCAAGGACCCCGTGGCTTGTTCAGGGGATGGATGGCCACACTGG


Block sizes: 39 (upstream exon), 32 (downstream exon)
Score: 10

GCCGCTGTTCTACGCTACCTGCGCCCTCGGCGGCGTTCTCAGCACCGGCCTCACTCACCTCGCTGTAACGCCGCTCGACCTCGTCAAGTGCAACATGCAGgtccgtcact ... cttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTCCATGAGCAAGGACCCCGTGGCTTGTTCAGGGGATGGATGGCCACACTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatgtctcaatgactaacacagctgctgcctgcttcaatgtcccttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTCCATGAGCAAGGACCCCGTGGCTTGTTCAGGGGATGGATGGCCACACTGG
             gactaac  putative branch site (score: 10)
                                          tcccttcactc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccgtcactgtcagcgataggttccttcgcttgttctccttgtccatgtctcaatgactaacacagctgctgcctgcttcaatgtcccttcactcagGTGGATCCTAGCAAGTACAGGGACATTACATCTGCCTTTGGTGTCATGCTCCATGAGCAAGGACCCCGTGGCTTGTTCAGGGGATGGATGGCCACACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA