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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaacaacgtagcggaggtaacagggttgtctgttactctgtttcattaacactgccacttatgtgtttgtgcattctaatacttaatttcctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG

Basic information

species Zea mays
transcript GRMZM2G162672_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g28200.2 (Oryza sativa), 3'ss of exon 12
tgaacaacgtagcggaggtaacagggttgtctgttactctgtttcattaacactgccacttatgtgtttgtgcattctaatacttaatttcct-ggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
| |   |   |       ||||   |      || |   | |     ||| | ||  |   | |   | |    |  |  | || | |||||| |||||||||||| |||||||| |||||||||||||||||||| |||||||| |||
taacttagaaaaaattcataacttaggaaaaagtcaaagtatggttgtaata-tgaaatggagggagtagcttctaatcctcctcattttccttggagcagTTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG

upper sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA07G18470.1 (Glycine max), 3'ss of exon 13
-----------------------tgaacaacgtagcgga-ggtaacagggttgtctgttactctgtttcattaacactgccacttatgtgtttgtgcatt-ctaatacttaatttcctgga----gcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
                       | || ||  | |   |   | |   |  ||     ||||| | |  |       | | |  | | |||| |    |  ||  | ||||   || ||      ||||||| |||| ||||| |||||||||||||| |||||||| |||||||||
gtaagtacagaattgcacacatgttaa-aatattgtatacaatcatgtgactgctgcatactc-gctaaaccgttctttctaaatttatgttagcatctcactggttcttatcatcttgtgccttgcagTTCAAGTATTTCCTCAAGGACCCTGTGAAATATGATGTTAAATATCAG

upper sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA18G43310.1 (Glycine max), 3'ss of exon 13
-------tgaacaacgtagcggaggtaacagggttgtctg---ttact--ctgtttcat-taacactgccacttatgtgtttgtgcatt-----ctaatacttaatttcctgga----gcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
       |  ||||     |  | || | |   |||| |    | |||  ||| | |||   | || |    || |   |||||    |     ||  || |||   || ||      ||||||| |||| |||||  ||||||||||||| |||||||| |||||||| 
ggtaaagtacacaattgcacacatgttaaaatattgtttacaatcactgactgctacatgctaaaccgttctttctaaatttgttagcttctcactggtatttatcatcttgtgccttgcaGTTCAAGTATTTCCTCCAGGACCCTGTGAAATATGATGTTAAATATCA-

upper sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA16G19390.1 (Glycine max), 3'ss of exon 5
-----tgaacaacgtagcggaggtaacagggttgtctgttact------ctgtttcattaacact-----gccacttatgtgtttgtg----catt---ctaatacttaatttcctgga----gcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
     |  ||||     |  | || | |   |||| |   |        ||| | |||  || ||     |    || |   ||| ||    |||    ||  | ||||   || ||      ||||||| |||| ||||  |||||||||||||| |||||||| |||||||||
gtaagtacacaattgcacacatgttaaaatattgtttacaatcatgtgactgctgcatacacgctaaaccgttctttctaaatttatgttagcatctcactggttcttatcatcttgtgccttgcagTTCAAGTATTTCCGCAAGGACCCTGTGAAATATGATGTTAAATATCAG

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|211036110|gb|FL230102.1|FL230102
EST:     ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAG                         TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
genomic: ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
EST: gi|71759623|gb|DR957560.1|DR957560
EST:     ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAG                         TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATAT---
genomic: ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
EST: gi|211036106|gb|FL230098.1|FL230098
EST:     ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAG                         TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAN
genomic: ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
EST: gi|71314948|gb|DR794088.1|DR794088
EST:     ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAG                         TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
genomic: ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
EST: gi|211036107|gb|FL230099.1|FL230099
EST:     ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAG                         TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
genomic: ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
EST: gi|71324982|gb|DR799184.1|DR799184
EST:     ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAG                         TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
genomic: ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
EST: gi|149110076|gb|EE293890.2|EE293890
EST:     ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAG                         TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
genomic: ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
EST: gi|161591339|gb|EY962175.1|EY962175
EST:     TTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGGTTCTTTCAG                         TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGT
genomic: TTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTG-TTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGT
EST: gi|71426127|gb|DR807177.1|DR807177
EST:     ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAG                         TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
genomic: ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
EST: gi|71763867|gb|DR961804.1|DR961804
EST:     ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAG                         TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
genomic: ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
EST: gi|32931186|gb|CF035998.1|CF035998
EST:     ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAG                         TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
genomic: ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
EST: gi|148929759|gb|EE285358.2|EE285358
EST:     ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAG                         TTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
genomic: ATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG

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), 48 (downstream exon)
Score: 125

GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 316

GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 82

GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 133

GTTACCTATTGAGCACCGGTAAGCTGTATTATGCCCTGGTGTTGCTTGGGCTAACAATTCCTCAGGTGTTCTTTCAGgtatacctga ... cctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaacactgccacttatgtgtttgtgcattctaatacttaatttcctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG
                                          tttcct  CT-rich tract
                            attctaatacttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaacaacgtagcggaggtaacagggttgtctgttactctgtttcattaacactgccacttatgtgtttgtgcattctaatacttaatttcctggagcagTTCCAGTACTTCCTGAAGGACCCTGTGAAGTATGATGTCAAATATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- aacaacg
- - - - - - - - - - - - - - - -tgttact
- - - - - - - - - - - - - - - - - - - - - - - - - -actgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcattc