RetrogeneDB ID: retro_mmul_2379

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:1102224..1102844(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000005282
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CKAP1
• Ensembl ID: ENSMMUG00000000523
• Aliases: None
• Description: None

Sequence

>retro_mmul_2379
ATGGAGGTGACGGGGGTGTCGGCACCCACGGTGACCGTTTTCATCAGCAGCTCCCTCAACACCTTCTGCTCAGAGAAGCA
GTACAGCCGCAGCCTCACCATGGCTGAGTTTAAGTGTAAACTGGAGTTGCTGGTGGGCATCCTGCTTCCTGCATGGAACT
GGAGCTGTATGGAGTTGACGACAAGTTCTACAGCAAGCTGGATCAAGAGGATGCGCTGCTGGGCTCCTACCCTGTAGATG
ACGGCCGCCGCATCCACCTCATTGACCACAGCGGCGCCCGCCTTGGTGACTATGAGGATGTGTCTTGGGTGGAGAAGTAC
ACGATCTCACAAGAAGCCTGCGACCAGAGGCAAGACACGGTTTGCTTCTTGCTGAAGTGCAGCAAGCTTGGCCGCTACAA
CGAGGAGCGGGCTCAGCAGGAGGCCGAGGCCGCCCAGCGCCTTGCCAAAGAGAAGACCCAGGCCAGCTCCATCCCCGTGG
GCAGCCGCTGTGAGGTGTGGGCGGCGGGACACCGGGGTACCATCATGTATGTAGGTCTCACAGATTTCAAGCCTGGTTAC
TGGATTGGTGTCCGCTATGATGAGCCACTGGGGAAAAACGATGGCAGTGTGAATGGGAAG

Alignment

ORF - retro_mmul_2379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.3 %
• Parental protein coverage: 86.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEVTGVSAPTVTVFISSSLNTFRSEKRYSRSLTIAEFKCKLELLVG-SPASCMELELYGVDDKFYSKLDQ
          MEVTGVSAPTVTVFISSSLNTF.SEK.YSRSLT.AEFKCKLELLVG..PASCMELELYGVDDKFYSKLDQ
Retrocopy MEVTGVSAPTVTVFISSSLNTFCSEKQYSRSLTMAEFKCKLELLVG<HPASCMELELYGVDDKFYSKLDQ

Parental  EDALLGSYPVDDGCRIHVIDHSGARLGEYEDVSRVEKYTISQEAYDQRQGTGRWAPRGSMCRRGGGQGRQ
          EDALLGSYPVDDG.RIH.IDHSGARLG.YEDVS.VEKYTISQEA.DQRQ.T.......S...R......Q
Retrocopy EDALLGSYPVDDGRRIHLIDHSGARLGDYEDVSWVEKYTISQEACDQRQDTVCFLLKCSKLGRYNEERAQ

Parental  GHCREASVRVRRRHGEASSIPVGSRCEVRAAGHSPRRGTVMYVGLTDFKPGYWIGVRYDEPLGKNDGSVN
          .....A..R.......ASSIPVGSRCEV.AAGH...RGT.MYVGLTDFKPGYWIGVRYDEPLGKNDGSVN
Retrocopy QEAEAAQ-RLAKEKTQASSIPVGSRCEVWAAGH---RGTIMYVGLTDFKPGYWIGVRYDEPLGKNDGSVN

Parental  GK
          GK
Retrocopy GK

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	0.56 RPM	18.60 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	58.47 RPM
SRP007412_cerebellum	0.39 RPM	18.86 RPM
SRP007412_heart	0.71 RPM	11.60 RPM
SRP007412_kidney	1.53 RPM	14.08 RPM
SRP007412_liver	0.44 RPM	11.60 RPM
SRP007412_testis	2.64 RPM	56.05 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2379 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2379 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015004	1 retrocopy	retro_btau_278,
Macaca mulatta	ENSMMUG00000000523	1 retrocopy	retro_mmul_2379 ,