RetrogeneDB ID: retro_mmul_2009

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:53845707..53846796(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030086
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C1GALT1
• Ensembl ID: ENSMMUG00000016338
• Aliases: None
• Description: None

Sequence

>retro_mmul_2009
ATGGCCTCTAAATCCTGGCTGAATTTTTTTACCTTCCTCTATGGATCGGCAATAGGATTTCTTTTATGTTCTCAGCTATT
TAGTATTTTGTTGGAAGAAGAGGGTGACACCCAGTCTGATGTTCTTCATAATGATCCTCATGTGAGGCATTCAGATGATA
ATGGACAGAATCATCTAGAAGGACAAATGAACTTCAATGCAGATTCTAGCCAACGTAAAGATGAGAACATAGACATCACT
GAAAACCTCTATCAGCAAGTTAAAATTCTTTGCTGGGTTATGACAGGCCCTCAAAACCTAGAGAAAAAGGCCAAACGTGT
CAAAGTTACCTGGGTCCAGCATAGTCACAAAGTGTTTTTTATGAGTTCGGAAGAAAATAAAGACTTCCCTGCTGTGGGAT
TGAAAACCAAAGAAGGCAGAGATCAGCTTTACTGGAAAACAATTAAACCTTTTCAGTATGTTCATGAACATCATTTAGAA
GATGTTGATTGGTTTTTGAAAGCAGATGATGATACATATTTTGTACTAGACAATTTGAGATGGCTTCTTTCAAAATATGA
TTCTAAAGAACCCATTTACTGTGGAAGAAGATTTAAACCCTTTGTAAAACAGGGCTATATGAGTGGAGGAGCAGCATATT
TACTAAGCAAAGAAGGCTTGAAGAGATTTGTTGATGCATTTAAAACAGACAAGTGTACACATAATTTCTCCATTGAAGAC
TTAGCACTGGGAAGATGCATGGAAATTATAAATGTAGAAGCAGGAGATTCCAGAGATGCCATTGGAAAAAAACCTTTTCA
TCCCTTTGTGCCAGAACACCACTTAATAAAGGTTATCTACTTAGAACCTTTTGGTACAGGAATTACAACTATTATCCTCC
TGTAGAGGGTCCTGGTTGCTGTTCTGATCTTGCAGATTCTTTTCACTATGTTGATTTTTACAACTGGGTATGTGTTAGAA
TACCTCATTTATCATCTTCGTCCGTATATTTATTTATACAGATATCAAGCTACCTTACCTGAAAATATACTAAAGGAAAT
TAGTCAAGCAAACAAAAATGAAGGCACAAAAGTGAAGTTAGGAAACCCT

Alignment

ORF - retro_mmul_2009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASKSWLNFLTFLCGSAIGFLLCSQLFSILLGEQGDIQPNVLHNDPHARHSDDNGQNHLEGEMNFNADSS
          MASKSWLNF.TFL.GSAIGFLLCSQLFSILL.E.GD.Q..VLHNDPH.RHSDDNGQNHLEG.MNFNADSS
Retrocopy MASKSWLNFFTFLYGSAIGFLLCSQLFSILLEEEGDTQSDVLHNDPHVRHSDDNGQNHLEGQMNFNADSS

Parental  QHKDENTDIAENLYQKVKILCWVMTGPQNLEKKAKHVKATWAQRCNKVLFMSSEENKDFPAVGLKTKEGR
          Q.KDEN.DI.ENLYQ.VKILCWVMTGPQNLEKKAK.VK.TW.Q...KV.FMSSEENKDFPAVGLKTKEGR
Retrocopy QRKDENIDITENLYQQVKILCWVMTGPQNLEKKAKRVKVTWVQHSHKVFFMSSEENKDFPAVGLKTKEGR

Parental  DQLYWKTIKAFQYVHEHYLEDADWFLKADDDTYVILDNLRWLLSKYDPEEPIYFGRRFKPYVKQGYMSGG
          DQLYWKTIK.FQYVHEH.LED.DWFLKADDDTY..LDNLRWLLSKYD..EPIY.GRRFKP.VKQGYMSGG
Retrocopy DQLYWKTIKPFQYVHEHHLEDVDWFLKADDDTYFVLDNLRWLLSKYDSKEPIYCGRRFKPFVKQGYMSGG

Parental  AGYVLSKEALKRFVDAFKTDKCTHSSSIEDLALGRCMEIINVEAGDSRDTTGKETFHPFVPEHHLI-KGY
          A.Y.LSKE.LKRFVDAFKTDKCTH..SIEDLALGRCMEIINVEAGDSRD..GK..FHPFVPEHHLI.KGY
Retrocopy AAYLLSKEGLKRFVDAFKTDKCTHNFSIEDLALGRCMEIINVEAGDSRDAIGKKPFHPFVPEHHLI<KGY

Parental  LPRTFWYWNYNYYPPVEGPGCCSDLAVSFHYVD-STTMYELEYLVYHLRPYGYLYRYQPTLPEDILKEIS
          L.RTFWY.NYNYYPPVEGPGCCSDLA.SFHYVD..TT.Y.LEYL.YHLRPY.YLYRYQ.TLPE.ILKEIS
Retrocopy LLRTFWYRNYNYYPPVEGPGCCSDLADSFHYVD>FTTGYVLEYLIYHLRPYIYLYRYQATLPENILKEIS

Parental  QANKKEDTKVKLGNP
          QANK.E.TKVKLGNP
Retrocopy QANKNEGTKVKLGNP

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	4.03 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.73 RPM
SRP007412_cerebellum	0.06 RPM	3.68 RPM
SRP007412_heart	0.00 RPM	2.36 RPM
SRP007412_kidney	0.00 RPM	6.34 RPM
SRP007412_liver	0.00 RPM	1.74 RPM
SRP007412_testis	0.00 RPM	14.36 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2009 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2009 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2009 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3177
Pan troglodytes	retro_ptro_2266

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000225	2 retrocopies	retro_chof_1782, retro_chof_2581,
Dasypus novemcinctus	ENSDNOG00000017353	2 retrocopies	retro_dnov_1801, retro_dnov_1905,
Homo sapiens	ENSG00000106392	2 retrocopies	retro_hsap_3177, retro_hsap_4065,
Loxodonta africana	ENSLAFG00000000063	1 retrocopy	retro_lafr_1166,
Myotis lucifugus	ENSMLUG00000014789	1 retrocopy	retro_mluc_1310,
Macaca mulatta	ENSMMUG00000016338	1 retrocopy	retro_mmul_2009 ,
Oryctolagus cuniculus	ENSOCUG00000026002	1 retrocopy	retro_ocun_216,
Otolemur garnettii	ENSOGAG00000012847	1 retrocopy	retro_ogar_855,
Petromyzon marinus	ENSPMAG00000001562	1 retrocopy	retro_pmar_2,
Pan troglodytes	ENSPTRG00000018925	2 retrocopies	retro_ptro_2266, retro_ptro_2755,