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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttttgtattattagcatataaattcttttctgtagtagtatataaaattctttgttgtctgggaactctccatgcagttcttttagtcttcactatgtaatttggttttttgctttggcttacattcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG

Basic information

species Zea mays
transcript GRMZM2G057576_T02
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 15
gtatcttttgtattattagcatataaattcttttctgtagtagtatataaaattctttgttgtctgggaactctccatgcagttcttttagtcttc-actatgtaatttggtt---ttttgctttggctta--cattcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG
                                       |||   | | || |  |||      ||   | ||   ||| | | | |||  | ||  || ||| ||||  |||   | |||| ||  | |   |||| || |||||||||| |||||||| ||||| |||||||| |||||||||||| | ||||||||||||||||| |||||||||||||||||||||
---------------------------------------gtatccttttaattcatttcaa---tgcatagtcggtatgtaatacctttgcttttttaccatgaaattcagttgtgtcttgccttaccatgcccattttttaacagAGAAACATGATACGTGAGGCAACAGCTTTCCTGCTGGATGTTTTAAAGCCAAACTTGCCGGAGCATGCTTTTCTTCAAACCAAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 15
gtatcttttgtattattagcatataaattcttttctgtagtagtatataaaattctttgttgtctgggaactctccatgcagttcttttagtcttcacta-tgtaatttggttttttgctttggcttacattcttcaa--cagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG----------------
                                        |  || ||||||  |    ||| |  |    ||  |      ||  |  |||  | | || ||  |    |||  ||  |||  |||   || | |    ||||||||| |||| || ||||| |||||||||||||| ||||||||||| |||||  | || || ||||  |  |||||||| |||                
----------------------------------------ttatacataaaaagcac--ttgcccagtctttcctctccttatttgtacagtaattattagtgctagacagttcatt-ttttacctttttttgtcctgttcagAGAAATCTGATCCGTGAGGCAACAGCTTTTCTGCTAGATGTTCTGAAACCAAATCTACCAGAACATGGGTACCTTCAAACTAAGGTGTTGGAGATAAATC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 15
gtatcttttgtattattagcatataaattcttttctgtagtagtatataaaattctttgttgtctgggaactctccatgcagttcttt-tagtcttcactatgtaatttggttttttgctttggcttacattcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG
||   || | | || | |  |   || || |  |   || ||  |||| | ||| ||    || |   ||   |  ||  ||| ||   | ||  |    || ||  ||| | |||| | || | |||| ||| |   ||||||||| |||| || ||||| ||||||||||| ||||||||| | ||||| ||  | || || ||||  || ||||| || |||
gttgattatatgttgtgattaagcaa-ttttgatgaatatta--atatgatattttt----gtttcataatcattgatttagtactgaatggttcttgaaat-ta--ttgttattttccatttggttac-ttcctgctcagAGAAATCTGATTCGAGAGGCAACAGCTTTTCTCCTGGATGTTTTAAAGCCGAATCTACCAGAACATGGGTTCCTTCAGACAAAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 15
gtatcttttgtattattagcatataaattcttttctgtagtagtatataaaattctttgttgtctgggaactctccatgcagttcttttagtcttcactatgtaatttggttttttgctttggcttacattcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG
||   || | | || | |  |   || || |  |   || ||  |||| | ||| ||| |  |      |   |  ||  ||| ||    |  |||   |  | |||    ||||   ||||| |||| |||| |  ||||||||| |||| || ||||||||||||||||| ||||||||| | ||||||||  | || || ||||  || ||||| || |||
gttgattatatgttgtgattaagcaa-ttatgatgaatatta--atatgatattttttttcat-----gatcattgatttagtactgaatgg-ttcttgaaattattgttattttcattttgg-ttactttctgct-cagAGAAATCTGATCCGAGAGGCTACAGCTTTTCTCCTGGATGTTTTAAAGCCAAATCTACCAGAACATGGGTTCCTTCAGACAAAG

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 15
gtatcttttgtattattagcatataaattcttttctgtagtagtatataaaattctttgttgtctgggaactctccatgcagttcttttagtcttcactatgtaatttggttttttgctttggcttacattcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG----------------
                            |||        | |   |   | ||  ||  |   ||      | |   | ||||  ||    |  |  |||   | |    || ||  ||||   ||    | ||||   ||||||| |||| || ||||| ||||| |||||||| ||||||||||| |||||  | || || ||||  |  |||||||| |||                
----------------------------tctacataaaggcaccttcccagatctttcctctcct------tatttttacagtaatt---attattgctagacagtacatttattaccttttttttgtcctgttca---gAGAAATCTGATCCGTGAGGCAACAGCCTTTCTGCTAGATGTTCTGAAACCAAATCTACCAGAACATGGGTACCTTCAAACAAAGGTGTTGGAGATAAATC

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatcttttgtattattagcatataaattcttttctgtagtagtatataaaattctttgttgtctgggaactctccatgcagttcttttagtcttcactatgtaatttggttttttgctttggcttacattcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG
                                    ||       || || || || |||    |   |      |       |  |||           | | || || |  | | |||    || |||  |    ||||||||| |||| || || || || ||||| || |||||||||||||||||||| || || || ||||||||||| ||||| |||
------------------------------------gtgaacacgtagaatatactgtgt-acataaaattgtatctcattacttgtttcacaagagagctatcatgtgctaatgtacttacttttgcatatt----cagAGAAATCTGATCCGTGAAGCGACTGCTTTCCTTCTGGATGTTCTGAAGCCAAATTTACCCGAGCATGCTTTTCTGCAAACTAAG

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), 48 (downstream exon)
Score: 233

GGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAGgtatcttttg ... tcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 125

GGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAGgtatcttttg ... tcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 89

GGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAGgtatcttttg ... tcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 230

GGAGCTGTCAACTTTGCATTGATGATGTCACAAATGGAGGGAGGTTGTCCAGTAGACTACAACACTATCACTGATCTCTTCCTTCAGgtatcttttg ... tcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagtcttcactatgtaatttggttttttgctttggcttacattcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG
                                    ggcttac  putative branch site (score: 230)
                                          cattcttc  CT-rich tract
                 taatttggtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcttttgtattattagcatataaattcttttctgtagtagtatataaaattctttgttgtctgggaactctccatgcagttcttttagtcttcactatgtaatttggttttttgctttggcttacattcttcaacagAGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC