RetrogeneDB ID: retro_mmul_630

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:36782583..36783427(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000009814
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.17875
• Ensembl ID: ENSMMUG00000014905
• Aliases: None
• Description: beta-galactoside alpha-2,6-sialyltransferase 1 [Source:RefSeq peptide;Acc:NP_001245009]

Sequence

>retro_mmul_630
AAAAGTACAGTGTCCTACAAGGGGCCAGGGCCCATTAAGTTCAGTGCAGAAGCCCTGCGCTGCCACCTCCTGGACCATGT
GAACGTATCCACAGTAGCGACCACAGATTTTCTCTTCAGTACCTCTTCGTAGGAGGGTTACCTGCCCGAGGGCAGCATTA
GGACCCAAGCCACGTCTTGGGGCAAGTGTGCTGTTTTCTCGTCAGCAGGATCTCTGAAGTCCTCGCAACTGGGCAGAGAT
CTAGATGATCATGATGCAGTCTTGAGGTTTAATGAGGCACCCACAGCCAACTTCCATCAAGATGTAGCCACAAAACTACC
ATTCGCCTGCTGAACTCTCAGTTGGTCACCACAAAAAGGCATTTCCTCAGAGACAGTCTGTACAATGAAGGAATCCTAAT
TGTATGGGACGCATCTATATATCATTCAGATATTTCAAAGTGGTACCAGAATCCAGACTATAATTTCTTTAATAACTACA
AGAGCTATCATAAGCTGCACCCCAATCTGCCCTTTTACATCCTCAAGTCCCAGGTGCCTTGGGAGTTGTGGGACATCCTG
CAAGAAATCTCCCTAGAAGAGATTCAGTGATGCCTCCATCCTCTGGGATACTTGGTGTCATTATCATGATGACGCTGTGT
GACCAGGTGGATATTTACAAGTTCCTACCATCCAAGCACGAGACAGACTTGGGCTGCTATCACCAGCAGTTCTTCAACAG
CGCCTGCACGATGGGCGCCCACCACCCGCTGCTGTATTTGGTGAAGTGCCTCTATGAGGGCACAGGTGAGGACATTTACC
TGCTTGGAAAAGCTACACTGCCTGGCTTCTGGGCCATTCACTGC

Alignment

ORF - retro_mmul_630 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.12 %
• Parental protein coverage: 70.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KYKVSYKGPGPGIKFSAEALRCHLRDHVNVSMVEATDFPFNTSEWEGYLPKDNIRTKAGPWGRCAVVSSA
          K..VSYKGPGP.IKFSAEALRCHL.DHVNVS.V..TDF.F.TS..EGYLP...IRT.A..WG.CAV.SSA
Retrocopy KSTVSYKGPGP-IKFSAEALRCHLLDHVNVSTVATTDFLFSTSS*EGYLPEGSIRTQATSWGKCAVFSSA

Parental  GSLKSSQLGREIDDHDAVLRFNGAPTANFQQDVGTK-TTIRLMNSQLVTTEKRFLKDSLYNEGILIVWDP
          GSLKSSQLGR..DDHDAVLRFN.APTANF.QDV.TK.TTIRL.NSQLVTT...FL.DSLYNEGILIVWD.
Retrocopy GSLKSSQLGRDLDDHDAVLRFNEAPTANFHQDVATK<TTIRLLNSQLVTTKRHFLRDSLYNEGILIVWDA

Parental  SVYHSDIPKWYQNPDYNFFNNYKSYRKLHPDQPFYILKPQMPWELWDILQEISPEEIQ-PNPPSSGMLGI
          S.YHSDI.KWYQNPDYNFFNNYKSY.KLHP..PFYILK.Q.PWELWDILQEIS.EEIQ...PPSSG.LG.
Retrocopy SIYHSDISKWYQNPDYNFFNNYKSYHKLHPNLPFYILKSQVPWELWDILQEISLEEIQ<VMPPSSGILGV

Parental  IIMMTLCDQVDIYEFLPSKRKTDVCYYYQKFFDSACTMGAYHPLLYEKNLVKHLNQGTDEDIYLLGKATL
          IIMMTLCDQVDIY.FLPSK..TD...Y.Q.FF.SACTMGA.HPLLY...LVK.L..GT.EDIYLLGKATL
Retrocopy IIMMTLCDQVDIYKFLPSKHETDLGCYHQQFFNSACTMGAHHPLLY---LVKCLYEGTGEDIYLLGKATL

Parental  PGFRTIHC
          PGF..IHC
Retrocopy PGFWAIHC

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	8.96 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	10.39 RPM
SRP007412_cerebellum	0.00 RPM	16.01 RPM
SRP007412_heart	0.06 RPM	6.36 RPM
SRP007412_kidney	0.12 RPM	16.90 RPM
SRP007412_liver	0.20 RPM	117.52 RPM
SRP007412_testis	0.00 RPM	0.41 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_630 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_630 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_630 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010357	1 retrocopy	retro_btau_1767,
Canis familiaris	ENSCAFG00000013698	1 retrocopy	retro_cfam_2158,
Felis catus	ENSFCAG00000013886	1 retrocopy	retro_fcat_1983,
Macaca mulatta	ENSMMUG00000014905	1 retrocopy	retro_mmul_630 ,
Nomascus leucogenys	ENSNLEG00000006676	1 retrocopy	retro_nleu_2774,
Pongo abelii	ENSPPYG00000014388	1 retrocopy	retro_pabe_3575,