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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaattattgggtgtacgtgtgtacaccaatacaccatgtcctttactcggtttgcccctcattgggatgatgggttgatatatttgttgattctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGCATGTGAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT

Basic information

species Zea mays
transcript GRMZM2G060870_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060870_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 1
aaaattattgggtgtacgtgtgtacaccaatacaccatgtcctttactcggtttgcccctcattg-ggatgatgggttgatatatttgttgattc---tttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGCATGTGAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT
   ||||     |||  ||| |  ||      |   |     ||     || ||     |   |  ||  |||  |||||   |||  ||| ||    || ||| |  | ||||||| ||||| |||||||| ||||| ||||| || ||||||||||| ||| |||||| | | ||||| |||||||||||||| ||||||||
---attagaaactgt-tgtgggatcagtgtctctttagtgaattagtgtggatttttgtttgctacggccgatatgttgacgcattcattgttttctattgcagCTAGAGAGATGGCCGAGACAGTGTTCACTCCCTCGTTGGAGGGTATGAAGCATGTTAAGTCAGAGAGCAGTGTCATACTCACCAAGCCCTTTCTTGATGT
















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|211301820|gb|FK983372.1|FK983372
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|32832496|gb|CD972174.1|CD972174
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211377987|gb|FK983378.1|FK983378
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211301817|gb|FK983369.1|FK983369
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211301822|gb|FK983374.1|FK983374
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|32867862|gb|CF007544.1|CF007544
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|78113898|gb|DV532287.1|DV532287
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|22542222|gb|BU092660.1|BU092660
EST:     TCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAAATGGCAGAGACGG-GTTCACCCCCTCTTTGGAAGGTATGAAGC
genomic: TCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211377984|gb|FK983375.1|FK983375
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211301814|gb|FK983366.1|FK983366
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAAATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGTATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211301815|gb|FK983367.1|FK983367
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACMAG                         GTTCATAGATGGCAGAGACGGTGTTCACCTSKCCTCTTTGGAAGGGATGAA
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACC--CCCTCTTTGGAAGGGATGAA
EST: gi|32866745|gb|CF006427.1|CF006427
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211377989|gb|FK983380.1|FK983380
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211453293|gb|FL230455.1|FL230455
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|87157246|gb|DY402035.1|DY402035
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAAATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGTATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|26559123|gb|CA831358.1|CA831358
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAAATGGCAGAGACGG-GTTCACCCCCTCTTTGGAAGGTATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211301812|gb|FK983364.1|FK983364
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211301816|gb|FK983368.1|FK983368
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211301818|gb|FK983370.1|FK983370
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211377986|gb|FK983377.1|FK983377
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
EST: gi|211453296|gb|FL230458.1|FL230458
EST:     CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAG                         GTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC
genomic: CAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGC

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), 49 (downstream exon)
Score: 124

GTGGAGCTACTAGGTGACCGTCGCGGCCGCCCTACGCCACGTGCTCGATCCAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGCATGTGAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 175

GTGGAGCTACTAGGTGACCGTCGCGGCCGCCCTACGCCACGTGCTCGATCCAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGCATGTGAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 88

GTGGAGCTACTAGGTGACCGTCGCGGCCGCCCTACGCCACGTGCTCGATCCAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGCATGTGAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 133

GTGGAGCTACTAGGTGACCGTCGCGGCCGCCCTACGCCACGTGCTCGATCCAGCCTCGTCGGCTTCTTCGCACCCGTCACCGGCGGTCAGCACCCACCAGgtattcgcac ... attctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGCATGTGAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcggtttgcccctcattgggatgatgggttgatatatttgttgattctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGCATGTGAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT
                                        tgttgat  putative branch site (score: 133)
                                              ttctttc  CT-rich tract
                                 atatatttgttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaattattgggtgtacgtgtgtacaccaatacaccatgtcctttactcggtttgcccctcattgggatgatgggttgatatatttgttgattctttcagGTTCATAGATGGCAGAGACGGTGTTCACCCCCTCTTTGGAAGGGATGAAGCATGTGAAGGCAGAGAACGGAGTCATTCTCACCAAGCCCTTCCTTGATGT

- - - - - - - - - - - tacacca
- - - - - - - - - - - - - - - - - -catgtcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgttg