RetrogeneDB ID: retro_mmul_1682

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:61329564..61330717(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: C15H9ORF140
• Ensembl ID: ENSMMUG00000007112
• Aliases: SAPCD2, C15H9orf140
• Description: None

Sequence

>retro_mmul_1682
GCCGAGCAGGGCTGCGTGTCTCCCGCCTAGCCCGCGCGCGGCACGGATGGGCTGCCGCGCGCCTTCCTGCAGAGCCTGCT
CACCCTGTTAGACATCCTGGACCACCGGCGGCGCGGCTGCTTGCACCTGCAAGAGATCCAGTCCCGCTGGCAGAGAGCCG
AAGCCCAGGGGCTGCCTAGCGGGGTGCTGAAAGGCCTGAGTCAGGTGGCCCCAGCTAGCTGCTACCTTACCTTCCAGCGC
TTCGTTGCCGGTCTGCGCACCTAGCTGCTGAGAGCCGATGGCCGCACCCGGGACCCCACGCGCGCCAGGGCCGGGCCCGG
AGACCAGCCGCCGCAGCGCCTGCTGTTTGCACCGGCTGTCGATCTGCTGACGGTCCTGGAGAGGAAGCCCCTGTCCCTGG
GCGTTCGCGCCGCTCTGACAGGTCCCAGAGGCCCGGCCCGCAGCCTGGAGCAGCTGTACGCCCCCGCCAAGGCGGCGCCC
TGCCCGGCAGAGCCCGAGTGGTCCCAGAGCGCGGCGGTGGAACGGAGTCAGGGCGCCGACGCAGGTGCAGCGGCCTGCAG
GGTCTTGGAGGCGGATTCAGGGGATGCCCGGCTGCCCCCCCGTGCCCGAGGGGAAGGTCGGAGGCACACCATCACCAGCG
GCGTGGACTGCGGCCTGCTGACGCAGATGTAGAAACTGGAGCAGGAGAGGGAGATGCTGCTGCAGGGTTTGGAGATGATG
GCGCCGGGCCGCAATTGGTACCAGCAGCAGCTGCAACGACTGCAGGAGTGCCAGTGCCGCCTGGGCCAGAGCAGAGCCAG
CGCCGACGTTGGGCTGTGGGGAGCCCTCGCCCACTGGGACGGCTACTGCCCAAAGTAGAGGAGGTGGCCCGGTGGCGGGG
GGAGCTGCTGGCTGCGGCCTGGGCCAGCCAGGCCCTGCTCACGTCCTCCTCCGGACCGCCTGCTCTGTCCTGACGTCCAC
CTTGTCTCCCGGATGGCAGCAGCAGATCATCCTCATGCTGAAGGAGCAGAATCGACTCCTCACCCAGGAGGTGACCGAGA
AGAGTGAGTGCATCACGCAGCTGGAGCAGGAGAAGTCGGCGCTCATTAAGCAGCTGTTTGAGGCCGGTGCCCTGAGCCAG
CAGGAGGCGAGGTCTCTGTACTCCACCTTCATC

Alignment

ORF - retro_mmul_1682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.41 %
• Parental protein coverage: 99.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AERGRVPPPAPAPGTEGLPRAFLQSLRTLFDILDDRRRGCVHLREIESRWQGTDARELPRGVLEGLRQVA
          AE.G.V.P..PA.GT.GLPRAFLQSL.TL.DILD.RRRGC.HL.EI.SRWQ...A..LP.GVL.GL.QVA
Retrocopy AEQGCVSPA*PARGTDGLPRAFLQSLLTLLDILDHRRRGCLHLQEIQSRWQRAEAQGLPSGVLKGLSQVA

Parental  PASGYLTFERFVAGLRTSLLSADGGPRDPTRAPARPGDQPPPPPQRLVFAPADEPRTVLERKPLPLGVRA
          PAS.YLTF.RFVAGLRT.LL.ADG..RDPTRA.A.PGDQ...PPQRL.FAPA....TVLERKPL.LGVRA
Retrocopy PASCYLTFQRFVAGLRT*LLRADGRTRDPTRARAGPGDQ---PPQRLLFAPAVDLLTVLERKPLSLGVRA

Parental  PLAGPSGAARSPEQLCAPAEAAPCPADPERSQSAALEPSSSADAGAVACRALEVDSGDARRAPRARGERR
          .L.GP.G.ARS.EQL.APA.AAPCPA.PE.SQSAA.E.S..ADAGA.ACR.LE.DSGDAR..PRARGE.R
Retrocopy ALTGPRGPARSLEQLYAPAKAAPCPAEPEWSQSAAVERSQGADAGAAACRVLEADSGDARLPPRARGEGR

Parental  RHTITSGVDCGLLKQMKELEQEKEVLLQGLEMMARGRDWYQQQLQRVQERQRRLGQSRASADCG-AAGSP
          RHTITSGVDCGLL.QM..LEQE.E.LLQGLEMMA.GR.WYQQQLQR.QE.Q.RLGQSRASAD.G.A.GSP
Retrocopy RHTITSGVDCGLLTQM*KLEQEREMLLQGLEMMAPGRNWYQQQLQRLQECQCRLGQSRASADVG<AVGSP

Parental  RPLGRLLPKVQEVARCLGELLAAACASRVLPPSSSGPP-CPALTSTSPLGWQQQTILMLKEQNRLLTQEV
          RPLGRLLPKV.EVAR..GELLAAA.AS..L..SSSGPP.C..LTST...GWQQQ.ILMLKEQNRLLTQEV
Retrocopy RPLGRLLPKVEEVARWRGELLAAAWASQALLTSSSGPP<CSVLTSTLSPGWQQQIILMLKEQNRLLTQEV

Parental  TEKSERITQLEQEKSALIKQLFEARALSQQDGGPLDSTFI
          TEKSE.ITQLEQEKSALIKQLFEA.ALSQQ....L.STFI
Retrocopy TEKSECITQLEQEKSALIKQLFEAGALSQQEARSLYSTFI

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	0.22 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.08 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.35 RPM
SRP007412_liver	0.00 RPM	0.51 RPM
SRP007412_testis	0.00 RPM	0.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1682 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1682 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1682 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000186193	2 retrocopies	retro_hsap_3734, retro_hsap_3738,
Macaca mulatta	ENSMMUG00000007112	1 retrocopy	retro_mmul_1682 ,
Nomascus leucogenys	ENSNLEG00000008908	2 retrocopies	retro_nleu_2867, retro_nleu_2939,
Pongo abelii	ENSPPYG00000019804	5 retrocopies	retro_pabe_3124, retro_pabe_3222, retro_pabe_3223, retro_pabe_3233, retro_pabe_3527,
Pan troglodytes	ENSPTRG00000021589	6 retrocopies	retro_ptro_2530, retro_ptro_2532, retro_ptro_2534, retro_ptro_2537, retro_ptro_2543, retro_ptro_2992,