RetrogeneDB ID: retro_mmul_1719

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:123944085..123945020(-)
• Located in intron of: ENSMMUG00000017311

Retrocopy information

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

Parental gene information

• Parental gene symbol: CIAPIN1
• Ensembl ID: ENSMMUG00000020472
• Aliases: None
• Description: None

Sequence

>retro_mmul_1719
ATGGCAGATTTTGGGATCTCTGCTGGCCAGTTTGTGGCAGTGGTCTCGGATAAGTCATCCCCAGTGGAGGCTCTGAAAGG
TCTGGTGGATAAGCTTCAAGTGTTAACTGGCAATGAGGGCCGCAGGTCTGTGGAAAACATCAACCAGCTGTTGCAGTCTG
CCCACAAAGAATCCAGCTTTGACATTATTTTGTCGGGTTTAGTCCTGGGAAGCACCACTCTGCACAGTGCTGAGATTTTG
ACTGAAATCGCCCGGATCCTTCGGCCTGGTGAATGTCTTTTTCTGAAAGAGTCAGTAGAGACAGCTGTAGATAACAATAG
CAAAGTGAAGACAGCATCTAAGCTATGTTCAGCCCTGACTCTTTCTGGTCTTATGGAAGTGAAAGAGCTGCAGTGGGAGC
CCCTAACCCCTGAGGAAGTACTGTCTGTTTGAGAATATCTGGTCATGAAAGTGACTGCCTGCTGTTTGTTCAGATCACAG
GCAAAAAACTAAACTTTGAAATGGGTTCTTCTAGTCAGCTTAAGCTTTCCATCACCAAGAAGTCTTCTCCTTCAGTGAAG
CCTGCTGTGGACCCTGCTGCTGCCAAGCTGTGGACCCTCTCGGCCAACGATATGGAAGACGACAGCATGGATCTCATTGA
CTCAGATGAGCTGCTGGATCCAAAAGATTTGAAGAAGCCAGATCTGGCTTCCCTGTGGGCTGCTTCTTGTGGAGAAGGGA
AAAAGAGGAAGGCCTGCAAGAACTGCACCTGGGGCCTTGCTGAAGAACTGGAAAAAGAGAAGGCGAGGGAACAGATAAGC
TCCCAACCCAAGTCGGCTTGTTGAAACTGCTACCTGGACGATGCCTTCCACTGTGCCAGCTGCCCCTACCTTGGGATGCC
AGGCTTCAAACCTGGGGAAAAGATGCTTCTGAGTGATAGCAATCTTCACGATGCC

Alignment

ORF - retro_mmul_1719 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.05 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADFGISAGQFVAVVWDKSSPVEALKGLVDKLQVLTGNEGHVSVENINQLLQSAHKESSFDIILSGLVPR
          MADFGISAGQFVAVV.DKSSPVEALKGLVDKLQVLTGNEG..SVENINQLLQSAHKESSFDIILSGLV..
Retrocopy MADFGISAGQFVAVVSDKSSPVEALKGLVDKLQVLTGNEGRRSVENINQLLQSAHKESSFDIILSGLVLG

Parental  STTLHSAEILAEIARILRPGGCLFLKEPVETAVDNNSKVKTASKLCSALTLSGLVEVKELQREPLTPEEV
          STTLHSAEIL.EIARILRPG.CLFLKE.VETAVDNNSKVKTASKLCSALTLSGL.EVKELQ.EPLTPEEV
Retrocopy STTLHSAEILTEIARILRPGECLFLKESVETAVDNNSKVKTASKLCSALTLSGLMEVKELQWEPLTPEEV

Parental  QSVREYL-GHESDHLLFVQITGKKPNFEVGSSSQLKLSITKKSSPSVKPAVDPAAAKLWTLSANDMEDDS
          .SV.EYL.GHESD.LLFVQITGKK.NFE.GSSSQLKLSITKKSSPSVKPAVDPAAAKLWTLSANDMEDDS
Retrocopy LSV*EYL<GHESDCLLFVQITGKKLNFEMGSSSQLKLSITKKSSPSVKPAVDPAAAKLWTLSANDMEDDS

Parental  MDLIDSDELLDPEDLKKPDPASLRAASCGEGKKRKACKNCTCGLA-ELEKEKSREQMSSQPKSACGNCYL
          MDLIDSDELLDP.DLKKPD.ASL.AASCGEGKKRKACKNCT.GLA.ELEKEK.REQ.SSQPKSAC.NCYL
Retrocopy MDLIDSDELLDPKDLKKPDLASLWAASCGEGKKRKACKNCTWGLAEELEKEKAREQISSQPKSAC*NCYL

Parental  GDAFRCASCPYLGMPAFKPGEKVLLSDSNLHDA
          .DAF.CASCPYLGMP.FKPGEK.LLSDSNLHDA
Retrocopy DDAFHCASCPYLGMPGFKPGEKMLLSDSNLHDA

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	0.11 RPM	26.22 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	30.86 RPM
SRP007412_cerebellum	0.52 RPM	23.83 RPM
SRP007412_heart	0.29 RPM	18.84 RPM
SRP007412_kidney	0.82 RPM	38.73 RPM
SRP007412_liver	0.20 RPM	11.88 RPM
SRP007412_testis	0.45 RPM	141.46 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1719 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1719 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1719 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012055	1 retrocopy	retro_cjac_2575,
Homo sapiens	ENSG00000005194	1 retrocopy	retro_hsap_1875,
Gorilla gorilla	ENSGGOG00000012402	1 retrocopy	retro_ggor_1372,
Macaca mulatta	ENSMMUG00000020472	1 retrocopy	retro_mmul_1719 ,
Monodelphis domestica	ENSMODG00000013522	1 retrocopy	retro_mdom_456,
Nomascus leucogenys	ENSNLEG00000002876	1 retrocopy	retro_nleu_1229,
Pongo abelii	ENSPPYG00000007388	2 retrocopies	retro_pabe_1260, retro_pabe_1556,
Pan troglodytes	ENSPTRG00000008155	1 retrocopy	retro_ptro_1258,