RetrogeneDB ID: retro_mmul_1360

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:67318342..67318881(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.148
• Ensembl ID: ENSMMUG00000019906
• Aliases: None
• Description: None

Sequence

>retro_mmul_1360
TTATCAATGAATACTTTTGGTACAAAAGAGCCCCTCTGTGTGAAGGACAGCTCGGTTGCAGCCAGATTTGAGTGCATGAG
GAAAGGATTTGATAAAATTAGAATGCAGAAGACTCCGGAAAGGGCTCCGCTTGGACATGAGCCCCGGCTACCCCATGTGT
TACTGCTACAGCTAGGAACAACTTTCTTCAGATCGCCTGGTCGCGAACTTAACCCAGAAGAAGATGAAGTTGGAGGACTA
AAATGCTTAATGTCAGAGACAATGGGTGATCAAGATGGAGCTCTGAAGACTGGGTGATTGGTGGCTGCATTGGTCACTGA
TGGAGAGCGCATGTTGAACCTCCTCAGTATCCTTATGTTCCTGCACATATTACAAAGTCTATGGGACACAGGGAGTTGTT
TTTGGTTCAACTTCAAGAAAAAGCCTTGCTTGCAATCCCTAAAAATTATAAGTCGGTAGATACACCGTTGTTTTAATTGT
ATGGCAGTGCACCGAGATGTGGACTCATCATTTCCAGTTTCCCTCAGCTGTTGAGCAGG

Alignment

ORF - retro_mmul_1360 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.51 %
• Parental protein coverage: 95.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGEL
          L...TFGTKEPL..KDSSVAARF..MR..FDKI.M..T.E.....HE.RLPHVLLLQLGTTFF..PG.EL
Retrocopy LSMNTFGTKEPLCVKDSSVAARFECMRKGFDKIRMQKTPERAPLGHEPRLPHVLLLQLGTTFFRSPGREL

Parental  NPGEDEVEGLKRLMTEILGRQDGVL-QDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQ
          NP.EDEV.GLK.LM.E..G.QDG.L..DWVI..CIG..WR...EPPQYPY.PAHITK...H..LFLVQLQ
Retrocopy NPEEDEVGGLKCLMSETMGDQDGAL<EDWVIGGCIGH*WRAHVEPPQYPYVPAHITKSMGHRELFLVQLQ

Parental  EKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSR
          EKAL.A.PKNYK.V..PLF.LY..AP..G.IISS.PQLLSR
Retrocopy EKALLAIPKNYKSVDTPLF*LYGSAPRCGLIISSFPQLLSR

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	136.14 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	86.87 RPM
SRP007412_cerebellum	0.00 RPM	109.32 RPM
SRP007412_heart	0.00 RPM	24.79 RPM
SRP007412_kidney	0.00 RPM	46.60 RPM
SRP007412_liver	0.00 RPM	11.28 RPM
SRP007412_testis	0.00 RPM	43.27 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1360 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1360 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1360 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Echinops telfairi	ENSETEG00000013634	1 retrocopy	retro_etel_622,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Macaca mulatta	ENSMMUG00000019906	1 retrocopy	retro_mmul_1360 ,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Pteropus vampyrus	ENSPVAG00000014583	2 retrocopies	retro_pvam_533, retro_pvam_711,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,
Tarsius syrichta	ENSTSYG00000014602	4 retrocopies	retro_tsyr_1685, retro_tsyr_1888, retro_tsyr_790, retro_tsyr_988,