RetrogeneDB ID: retro_mmul_2319

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:15543067..15543469(-)
• Located in intron of: ENSMMUG00000007068

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLTA
• Ensembl ID: ENSMMUG00000006132
• Aliases: None
• Description: None

Sequence

>retro_mmul_2319
GAAATTAATGGTCCAAGAGACAATTATGCAGCTATTTCACAAGTGGATCGATTCTAATCACAGCCTGAAAATATTTGCAA
ATGGAAAGAAGAGAAAATGGAACGCTTAGAAGCACTTGCTGGCTATTCTCAGAAGCAAGAAGCAGAGTGGAAAGAAAACA
TGAAAAAGGAGCTGGCAGAGTGGTGTGCAAGACAAGACGAGCAGCTACAGAAAACAAAGGCAAACAACAAAGGGCAAAGG
GCAGAAGATTTTGTAAATGACTTTGATGAGTCATCCCCCAGCACTGAGTGGCATCAAGTGGCCTGGCTGTGTGACTGTAA
CCCCAGGTCCAGCAAGCAGGCCGAAGAGGTCCCCCGCACACACTCAGTCCTCAGCTCCCTCGGGCAGGCACCCCTGGTGC
AC

Alignment

ORF - retro_mmul_2319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.9 %
• Parental protein coverage: 61.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESNGPTDSYAAISQVDRLQSEPESIRKWREEQMERLEALDANSRKQEAEWKEKAIKELEEWYARQDEQLQ
          E.NGP.D.YAAISQVDR..S.PE.I.KW.EE.MERLEAL...S.KQEAEWKE...KEL.EW.ARQDEQLQ
Retrocopy EINGPRDNYAAISQVDRF*SQPENICKWKEEKMERLEALAGYSQKQEAEWKENMKKELAEWCARQDEQLQ

Parental  KTKANNRAAE-EAFVNDIDESSPGTEWERVARLCDFNPKSSKQAKDVSRMRSVLISLKQAPLVH
          KTKANN.....E.FVND.DESSP.TEW..VA.LCD.NP.SSKQA..V.R..SVL.SL.QAPLVH
Retrocopy KTKANNKGQRAEDFVNDFDESSPSTEWHQVAWLCDCNPRSSKQAEEVPRTHSVLSSLGQAPLVH

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	69.58 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	74.49 RPM
SRP007412_cerebellum	0.13 RPM	62.12 RPM
SRP007412_heart	0.06 RPM	28.27 RPM
SRP007412_kidney	0.00 RPM	103.99 RPM
SRP007412_liver	0.00 RPM	38.28 RPM
SRP007412_testis	0.04 RPM	21.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2319 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2319 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2319 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001137	1 retrocopy	retro_btau_327,
Homo sapiens	ENSG00000122705	2 retrocopies	retro_hsap_4022, retro_hsap_955,
Macropus eugenii	ENSMEUG00000010858	1 retrocopy	retro_meug_480,
Macaca mulatta	ENSMMUG00000006132	2 retrocopies	retro_mmul_2319 , retro_mmul_785,
Monodelphis domestica	ENSMODG00000002610	1 retrocopy	retro_mdom_1148,
Nomascus leucogenys	ENSNLEG00000003874	1 retrocopy	retro_nleu_659,
Pongo abelii	ENSPPYG00000019069	1 retrocopy	retro_pabe_3300,
Pan troglodytes	ENSPTRG00000020930	1 retrocopy	retro_ptro_2727,