RetrogeneDB ID: retro_mmul_1793

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:127427652..127428431(+)
• Located in intron of: ENSMMUG00000016373

Retrocopy information

• Ensembl ID: ENSMMUG00000029439
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.12832
• Ensembl ID: ENSMMUG00000017590
• Aliases: ARL14EP, C14H11orf46
• Description: None

Sequence

>retro_mmul_1793
ATGATGGATCCATGTTCAGTTGAAGTCCAGCTTCGTACTACAAATGAATGCCATAAAACCTACTATACTCGTCACACAGG
TTTTAAGACTTTGCAAGAATTGTCATCAAATGATATGCTTTTACTTCAACTTAGAACTGGAATGACACTTTCTGGGAACA
ATGCAATTTGCTTTCATCATGTAAAAATTTACATTGACAGATTTGAGGATTTACAGAAGTCATGTTATGACCCATTTAAC
ATACACAAAAAATTAGCCAAAAAAAATTTGCACATAATTGACTTAGATGATGCCACTTTTCTGAGTGCAAAATTCGGAAG
ACAGCTTGTACCTGGTTGGAAGCTTTGTCCAAAATGCACACAGATATCAATGGAAGTGTGGATGTTGATACTGAAGACTG
CCAGAAAAGGAAACCTGAGTCAGATGGAAGAACTGCTAAAGCTTTGAGGTCACTACAATTTACAAATCCAGGGAGGCAAA
CTGGATTTGCTCCAGAAACTGGTAAAAGAGAAAAAAGAAGGCTTACAAAAAATGCAACCGCTAGTTCAGACAGACAAGTG
ATAACAGCAAAGAGTAAGGTCTGTGATAGCCAAGGTCTCCTGATTTTTAGTGGGATGGACCTCTGTGACTGCCTCGATGA
AGATTGCTTAGGATGTTTCTATGCTTGTCCTGCCTGTGGTTCTACCAAGTGTGGAGCTGAATGCCGCTGTTACCACAAGT
GGCTGTATGAGCAAATTGAAATTGAAGGAGGAGAAATAATTCATAATAAACATGCTGGA

Alignment

ORF - retro_mmul_1793 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMDPCSVGVQLRTTNECHKTYYTRHTGFKTLQELSSNDMLLLQLRTGMTLSGNNTICFHHVKIYIDRFED
          MMDPCSV.VQLRTTNECHKTYYTRHTGFKTLQELSSNDMLLLQLRTGMTLSGNN.ICFHHVKIYIDRFED
Retrocopy MMDPCSVEVQLRTTNECHKTYYTRHTGFKTLQELSSNDMLLLQLRTGMTLSGNNAICFHHVKIYIDRFED

Parental  LQKSCCDPFNIHKKLAKKNLHVIDLDDATFLSAKFGRQLVPGWKLCPKCTQI-INGSVDVDTEDRQKRKP
          LQKSC.DPFNIH.......LH.IDLDDATFLSAKFGRQLVPGWKLCPKCTQI.INGSVDVDTED.QKRKP
Retrocopy LQKSCYDPFNIHXXXXXXXLHIIDLDDATFLSAKFGRQLVPGWKLCPKCTQI<INGSVDVDTEDCQKRKP

Parental  ESDGRTAKALRSLQFTNPGRQTEFAPETGKREKRRLTKNATAGSDRQVIPAKSKVYDSQGLLIFSGMDLC
          ESDGRTAKALRSLQFTNPGRQT.FAPETGKREKRRLTKNATA.SDRQVI.AKSKV.DSQGLLIFSGMDLC
Retrocopy ESDGRTAKALRSLQFTNPGRQTGFAPETGKREKRRLTKNATASSDRQVITAKSKVCDSQGLLIFSGMDLC

Parental  DCLDEDCLGCFYACPACGSTKCGAECRCDRKWLYEQIEIEGGEIIHNKHAG
          DCLDEDCLGCFYACPACGSTKCGAECRC..KWLYEQIEIEGGEIIHNKHAG
Retrocopy DCLDEDCLGCFYACPACGSTKCGAECRCYHKWLYEQIEIEGGEIIHNKHAG

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	9.75 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	11.03 RPM
SRP007412_cerebellum	0.19 RPM	11.95 RPM
SRP007412_heart	0.00 RPM	11.07 RPM
SRP007412_kidney	0.00 RPM	10.45 RPM
SRP007412_liver	0.00 RPM	10.01 RPM
SRP007412_testis	0.08 RPM	13.53 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1793 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1793 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1793 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012417	1 retrocopy	retro_btau_1266,
Choloepus hoffmanni	ENSCHOG00000012698	1 retrocopy	retro_chof_1155,
Felis catus	ENSFCAG00000028620	1 retrocopy	retro_fcat_437,
Microcebus murinus	ENSMICG00000011547	2 retrocopies	retro_mmur_1003, retro_mmur_131,
Macaca mulatta	ENSMMUG00000017590	2 retrocopies	retro_mmul_1793 , retro_mmul_984,
Mus musculus	ENSMUSG00000027122	1 retrocopy	retro_mmus_3319,