RetrogeneDB ID: retro_mmul_36

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214739930:4647..5886(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000002249
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000002247
• Aliases: None
• Description: None

Sequence

>retro_mmul_36
ATGGCTAACGTGGCTGACACGAAGCTGTACGACATCCTGGGCGTCCCGCCCGGCGCCAGCGAGAACGAGCTGAAGAAGGC
ATACAGAAAGTTAGCCAAGGAATATCATCCTGATAAGAATCCAAATGCAGGAGACAAATTTAAAGAAATAAGTTTTGCAT
ATGAAGTACTATCAAATCCTGAGAAGCGTGAGTTATATGACAGATACGGAGAGCAAGGTCTTCGGGAAGGCAGCGGCGGA
GGTGGTGGCATGGATGATATTTTCTCTCACATTTTTGGTGGGGGATTGTTCGGCTTCATGGGCAATCAGAGTCGAAGTCG
AAATGGCAGAAGAAGAGGAGAGGACATGATGCATCCACTCAAAGTATCATTAGAAGATCTGTATAATGGCAAGACAACCA
AACTCCAACTTAGCAAGAATGTACTCTGTAGTGCATGCAGTGGCCAAGGTGGAAAGTCTGGAGCTGTCCAGAAGTGTAGT
GCTTGTCGAGGTCGGGGTGTGCGCATCATGATCAGACAGCTGGCTCCAGGAATGGTACAACAGATGCAGTCTGTATGCTC
TGATTGTAATGGAGAAGGAGAGGTAATTAATGAAAAAGACCGCTGTAAAAAATGTGAAGGGAAGAAGGTGATTAAAGAAG
TGAAGATTCTTGAAGTCCACGTAGACAAAGGCATGAAACATGGACAGAGAATTACATTCACTGGGGAAGCAGACCAGGCC
CCAGGAGTGGAACCTGGAGACATTGTTCTTTTGCTACAGGAGAAAGAACATGAGGTATTTCAGAGAGATGGGAATGATTT
GCACATGACATATAAAATAGGACTTGTTGAAGCTCTGTGTGGATTTCAGTTCACGTTTAAGCACCTTGATGGACGTCAGA
TTGTGGTGAAATACCCCCCTGGCAAAGTAATTGAACCAGGATGTGTTCGTGTAGTTCGAGGTGAAGGGATGCCGCAGTAT
CGTAATCCCTTTGAAAAAGGTGATCTTTACATAAAGTTTTATGTGCAGTTTCCTGAAAACAACTGGATCAACCCAGACAA
GCTTTCCGAACTAGAAGATCTTCTGCCATCTAGACCGGAAGTTCCTAACATAATTGGAGAAACAGAGGAGGTAGAGCTTC
AGGAATTTGATAGCACTCGAGGCTCAGGAGGTGGTCAGAGGCGTGAAGCCTATAATGATAGCTCTGATGAAGAAAGCAGC
AGCCATCATGGACCTGGAGTGCAGTGTGCCCATCAGTAA

Alignment

ORF - retro_mmul_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANVADTKLYDILGVPPGASENELKKAYRKLAKEYHPDKNPNAGDKFKEISFAYEVLSNPEKRELYDRYG
          MANVADTKLYDILGVPPGASENELKKAYRKLAKEYHPDKNPNAGDKFKEISFAYEVLSNPEKRELYDRYG
Retrocopy MANVADTKLYDILGVPPGASENELKKAYRKLAKEYHPDKNPNAGDKFKEISFAYEVLSNPEKRELYDRYG

Parental  EQGLREGSGGGGGMDDIFSHIFGGGLFGFMGNQSRSRNGRRRGEDMMHPLNKLTFEYHSNGNICAVQFFM
          EQGLREGSGGGGGMDDIFSHIFGGGLFGFMGNQSRSRNGRRRGEDMMHPL.K...E...NG.....Q...
Retrocopy EQGLREGSGGGGGMDDIFSHIFGGGLFGFMGNQSRSRNGRRRGEDMMHPL-KVSLEDLYNGKTTKLQ--L

Parental  FKEMLCYIISTQGGKSGAVQKCSACRGRGVRIMIRQLAPGMVQQMQSVCSDCNGEGEVINEKDRCKKCEG
          .K..LC...S.QGGKSGAVQKCSACRGRGVRIMIRQLAPGMVQQMQSVCSDCNGEGEVINEKDRCKKCEG
Retrocopy SKNVLCSACSGQGGKSGAVQKCSACRGRGVRIMIRQLAPGMVQQMQSVCSDCNGEGEVINEKDRCKKCEG

Parental  KKVIKEVKILEVHVDKGMKHGQRITFTGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLHMTYKIGLVE
          KKVIKEVKILEVHVDKGMKHGQRITFTGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLHMTYKIGLVE
Retrocopy KKVIKEVKILEVHVDKGMKHGQRITFTGEADQAPGVEPGDIVLLLQEKEHEVFQRDGNDLHMTYKIGLVE

Parental  ALCGFQFTFKHLDGRQIVVKYPPGKVIEPGCVRVVRGEGMPQYRNPFEKGDLYIKFDVQFPENNWINPDK
          ALCGFQFTFKHLDGRQIVVKYPPGKVIEPGCVRVVRGEGMPQYRNPFEKGDLYIKF.VQFPENNWINPDK
Retrocopy ALCGFQFTFKHLDGRQIVVKYPPGKVIEPGCVRVVRGEGMPQYRNPFEKGDLYIKFYVQFPENNWINPDK

Parental  LSELEDLLPSRPEVPNIIGETEEVELQEFDSTRGSGGGQRREAYNDSSDEESSSHHGPGVQCAHQ
          LSELEDLLPSRPEVPNIIGETEEVELQEFDSTRGSGGGQRREAYNDSSDEESSSHHGPGVQCAHQ
Retrocopy LSELEDLLPSRPEVPNIIGETEEVELQEFDSTRGSGGGQRREAYNDSSDEESSSHHGPGVQCAHQ

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	7.51 RPM	16.58 RPM
SRP007412_brain_prefrontal_cortex	10.07 RPM	20.71 RPM
SRP007412_cerebellum	4.07 RPM	10.59 RPM
SRP007412_heart	5.24 RPM	9.72 RPM
SRP007412_kidney	4.34 RPM	8.80 RPM
SRP007412_liver	3.09 RPM	4.16 RPM
SRP007412_testis	6.52 RPM	6.11 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_36 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_36 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_36 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003757	3 retrocopies	retro_btau_1215, retro_btau_1625, retro_btau_798,
Cavia porcellus	ENSCPOG00000006955	1 retrocopy	retro_cpor_1466,
Dasypus novemcinctus	ENSDNOG00000013794	1 retrocopy	retro_dnov_40,
Macaca mulatta	ENSMMUG00000002247	1 retrocopy	retro_mmul_36 ,
Macaca mulatta	ENSMMUG00000007740	6 retrocopies	retro_mmul_1313, retro_mmul_1802, retro_mmul_2477, retro_mmul_2482, retro_mmul_2625, retro_mmul_400,
Oryctolagus cuniculus	ENSOCUG00000004839	1 retrocopy	retro_ocun_1126,
Rattus norvegicus	ENSRNOG00000016251	1 retrocopy	retro_rnor_2778,
Ictidomys tridecemlineatus	ENSSTOG00000004007	1 retrocopy	retro_itri_343,