RetrogeneDB ID: retro_mmul_64

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:43236489..43236936(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030700
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MRPL27
• Ensembl ID: ENSMMUG00000017231
• Aliases: None
• Description: None

Sequence

>retro_mmul_64
ATGGCGTCTGTGGTGCTGGCGCTGAGGACTCAGACAGCCGTTACATCCTTGCTGAGCTCCACTCCTGCTACAGCTCTTGC
TGTCAGATATGCATCCAAGAAGACAGGTGGTAGCTCCAAAAGCCTTGGTGGAAAGTCATCAGGCAGATGCCTAGGCATTA
ATAAAATGGAAGGTCACTATGTTCATGCTGGGAACATCATTGGAACACAGAACCATTTCCGCTGGCACCCAGGTGCCCAT
GTGGGTCTTGGGAAGAATAAATGTCTGTATGCCCTGGAAGAGGGGATAGTCCACTACACTAAGGAGGTCTACGTGCCTCA
TCTCAGAAACACGGAGGCTGTGGATCTGATCACCAGGCTGCCCAAGGGTGCTGTGCTCTTCAAGAATTTTGTCCACGTGG
TTCTTGCCAAGCTGGAGGGCACCTTCAAACTGGTAGCTATGCTTTGA

Alignment

ORF - retro_mmul_64 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASVVLALRTRTAVTSLLSSTPATALAVRYASKKSGGSSRNLGGKSSGKRLGIKKMEGHYVHAGNIIGTQ
          MASVVLALRT.TAVTSLLSSTPATALAVRYASKK.GGSS..LGGKSSG..LGI.KMEGHYVHAGNIIGTQ
Retrocopy MASVVLALRTQTAVTSLLSSTPATALAVRYASKKTGGSSKSLGGKSSGRCLGINKMEGHYVHAGNIIGTQ

Parental  RHFRWHPGAHVGLGKNKCLYALEEGIVRYTKEVYVPHPRNTEAVDLITRLPKGAVLYKTFVHVVPAKPEG
          .HFRWHPGAHVGLGKNKCLYALEEGIV.YTKEVYVPH.RNTEAVDLITRLPKGAVL.K.FVHVV.AK.EG
Retrocopy NHFRWHPGAHVGLGKNKCLYALEEGIVHYTKEVYVPHLRNTEAVDLITRLPKGAVLFKNFVHVVLAKLEG

Parental  TFKLVAML
          TFKLVAML
Retrocopy TFKLVAML

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	27.68 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	40.62 RPM
SRP007412_cerebellum	0.13 RPM	29.25 RPM
SRP007412_heart	0.06 RPM	21.02 RPM
SRP007412_kidney	0.00 RPM	29.69 RPM
SRP007412_liver	0.00 RPM	28.74 RPM
SRP007412_testis	0.04 RPM	18.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_64 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_64 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_64 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017031	1 retrocopy	retro_cfam_1454,
Choloepus hoffmanni	ENSCHOG00000005103	1 retrocopy	retro_chof_943,
Callithrix jacchus	ENSCJAG00000018851	2 retrocopies	retro_cjac_28, retro_cjac_378,
Dasypus novemcinctus	ENSDNOG00000023845	2 retrocopies	retro_dnov_1233, retro_dnov_1731,
Erinaceus europaeus	ENSEEUG00000010549	3 retrocopies	retro_eeur_126, retro_eeur_22, retro_eeur_9,
Echinops telfairi	ENSETEG00000014252	2 retrocopies	retro_etel_13, retro_etel_893,
Microcebus murinus	ENSMICG00000009698	1 retrocopy	retro_mmur_624,
Macaca mulatta	ENSMMUG00000017231	1 retrocopy	retro_mmul_64 ,
Mus musculus	ENSMUSG00000024414	2 retrocopies	retro_mmus_1696, retro_mmus_2918,
Oryctolagus cuniculus	ENSOCUG00000004601	2 retrocopies	retro_ocun_1026, retro_ocun_1936,
Otolemur garnettii	ENSOGAG00000005385	1 retrocopy	retro_ogar_53,