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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgacctatcagcctcgccggcgcgcgctgtttttctggctgcagcttccccataggtcagtagtatgcttttcttggcgtgtctgactgggggtcttcgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGC

Basic information

species Zea mays
transcript GRMZM2G411333_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G411333_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g27360.2 (Oryza sativa), 3'ss of exon 1
gtaggtgacctatcagcctcgccggcgcgcgctgtttttctggctgcagcttccccataggtcagtagtatgcttttcttggcgtgtctgactgggggtcttcgcag---cacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGC
            | ||  |  |||  ||   |  ||  ||  ||||  ||   |||    |   || |  ||| ||  |    |     |   ||| |    ||  |   | ||| || |||| ||| ||||| | ||||||| ||||| | ||| ||||||||||||||||||||||||||||||| |||||||||||||||||| ||  ||||
-----------gtaagttttaccgaagctttcccttagtcgtgctg-ggcgcgcccgcgcgcgcgt-gcgtgcgttcgtctctgatctcggtggggagcacacgggggggcgcagGCTCTACTTCACGCGGATTGGGATCGGCACGCCGGCGAAGCGCTACTACGTGCAGGTGGACACCGGCAGCGACATCCTCTGGGTCAACTGCGTCTCCTGC
















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|91051045|gb|EB161463.1|EB161463
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCC-ACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
EST: gi|71443428|gb|DR824478.1|DR824478
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
EST: gi|71329431|gb|DR801432.1|DR801432
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
EST: gi|94472394|gb|EB701352.1|EB701352
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
EST: gi|148946390|gb|EC891698.2|EC891698
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
EST: gi|71309094|gb|DR790817.1|DR790817
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
EST: gi|31356527|gb|CD440884.1|CD440884
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
EST: gi|71438608|gb|DR819658.1|DR819658
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
EST: gi|148962846|gb|EE013768.2|EE013768
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
EST: gi|50335617|gb|CO530743.1|CO530743
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
EST: gi|149010274|gb|EE042101.2|EE042101
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
EST: gi|91048431|gb|EB158849.1|EB158849
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
EST: gi|211421716|gb|FK968879.1|FK968879
EST:     GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGG                         CCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT
genomic: GGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGT

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: 48 (upstream exon), 38 (downstream exon)
Score: 16

ACCTCGCGGCGCTGCGGAGGCATGACGCCAACCGCCACGGCCGGCTCCTTGGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 34

ACCTCGCGGCGCTGCGGAGGCATGACGCCAACCGCCACGGCCGGCTCCTTGGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

ACCTCGCGGCGCTGCGGAGGCATGACGCCAACCGCCACGGCCGGCTCCTTGGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 40

ACCTCGCGGCGCTGCGGAGGCATGACGCCAACCGCCACGGCCGGCTCCTTGGCGCCGTCGACTTGGCCCTCGGCGGCGTCGGGCTCCCCACAGATACCGGgtaggtgacc ... cgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggtcagtagtatgcttttcttggcgtgtctgactgggggtcttcgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGC
                            gtctgac  putative branch site (score: 40)
                                         tcttcgc  putative PPT
                ttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtgacctatcagcctcgccggcgcgcgctgtttttctggctgcagcttccccataggtcagtagtatgcttttcttggcgtgtctgactgggggtcttcgcagcacagCCTGTACTACACCCGGATCGAGATCGGCTCGCCGCCCAAGGGCTACTACGTGCAGGTGGACACCGGCAGCGATATCCTCTGGGTCAACTGCATCCGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA