Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccagtgttgtctatcgcccttatatttttttttctaaagttaacagctggtgtggtgcgaagcatttgtgtaaccaattgcttggtttttgcctttacttgcctgctttttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG

Basic information

species Zea mays
transcript GRMZM2G064753_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064753_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
gtaagccagtgttgtctatcgcccttatatttttttttctaaagttaacagctggtgtggtgcgaagcatttgtgtaaccaattgcttggtttttgcctttacttgcctgctttttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG
             |||  ||    ||   ||   |   | |||  |   | |||        | ||  |||  || ||         |||| |   | |||  |  | | ||||   |  |||||||||| || |||||||||||||||||||||||||||||||| ||||||||||| |||||||| || ||||| ||||||
-------------gtcagtcagtgttgacttggctcagcgaaaactctaaactg--------ccaaatatt-atgcaata------ctggtatcaacattttttcactt-ctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
















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|211282257|gb|FL038859.1|FL038859
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|40334748|gb|CK368818.1|CK368818
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|60394469|gb|DN227339.1|DN227339
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|60341353|gb|DN208326.1|DN208326
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|71446669|gb|DR827719.1|DR827719
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|211158395|gb|FK955819.1|FK955819
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATG
EST: gi|211235602|gb|FL469489.1|FL469489
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|211161585|gb|FK955846.1|FK955846
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCC-TGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|101401433|gb|EB822394.1|EB822394
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|60343233|gb|DN210206.1|DN210206
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|60340030|gb|DN207003.1|DN207003
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|211282256|gb|FL038858.1|FL038858
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|32802685|gb|CD954921.1|CD954921
EST:     TGAGTCCTACTATACCAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|24763662|gb|CA398833.1|CA398833
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|211101980|gb|FL478954.1|FL478954
EST:     CTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: CTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|211282259|gb|FL038861.1|FL038861
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|32804663|gb|CD956899.1|CD956899
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|60353974|gb|DN220947.1|DN220947
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|32790022|gb|CD942258.1|CD942258
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|24768560|gb|CA403689.1|CA403689
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|5108358|gb|AI740071.1|AI740071
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACNCGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|44901526|gb|CK828071.1|CK828071
EST:     TGAGTCCTACTATAACAAGAGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|101401431|gb|EB822393.1|EB822393
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|60398986|gb|DN231802.1|DN231802
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
EST: gi|78026436|gb|DV494823.1|DV494823
EST:     TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAG                         AGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG
genomic: TGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATG

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: 144

GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 189

GAGGAACCATCTGTAGTTGAGTCCTACTATAACAAGCGGATAGTCGGCTGCCCTGGTGGTGAGGGAGgtaagccagt ... tttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtgtaaccaattgcttggtttttgcctttacttgcctgctttttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG
    gtgtaac  putative branch site (score: 189)
                      tttttgcctttacttg  putative PPT
                              tttactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccagtgttgtctatcgcccttatatttttttttctaaagttaacagctggtgtggtgcgaagcatttgtgtaaccaattgcttggtttttgcctttacttgcctgctttttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG