RetrogeneDB ID: retro_mmul_595

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:25490758..25491403(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDHD2
• Ensembl ID: ENSMMUG00000010999
• Aliases: None
• Description: None

Sequence

>retro_mmul_595
TTTGTGACCAATACGACCAAAGAGAGCAAGCAAGACCTGTTGCAAAGGTTGAGAAAATTGGAATTTGATATCTCTGAAAA
TGAAATATTCACATCTCTGACTGCAGCCAGAAGTTTACTAAAGCAGAAACAAGTCAGACCCATGCTGCTAGTTGATGATC
GGGCACTACCTGATTTCAAAGGAATACAAACAAGTGATCCTAATGCTGTGGTCATAGGATTGTCACCAGAACATTTTCAT
TATCAAATTCTGAATCAAGCATTCTGGTTACTCCTGGATGGAGCACCTCTGATAGCAATCCACAAAGCCAGGTATTACAA
GAGGAAAGATGGCTTAGCCCTGGGGCCTGGACCATTTGTGACTGCTTTAGAGTATGCCACAGATACCAAAGCCACAGTCG
TGGAGAAACCCGAGACGTTCTTTTTGGAAGCATTGCGAGGCACTGGCTGTGAACCTGAGGAGGCTGTCATGATAGGAGAT
GATTGCAGGGATGATGTTGGTGGGGCTCAGGATGTTGGCATGCTGGGCATCTTAGTAAAGACTGGGAAATACTGAGCATC
AGATGAAGAAAAAATTAATCCACCTCCTTACTTAACTTATGAGAGTTTCCCTCATGCTGTGGACCACATTCTGCAGCACC
TGTTG

Alignment

ORF - retro_mmul_595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.3 %
• Parental protein coverage: 82.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FVTNTTKESKQDLLERLRKLEFDISENEIFTSLTAARSLLEQKQVRPMLLVDDRALPDFKGIQTSDPNAV
          FVTNTTKESKQDLL.RLRKLEFDISENEIFTSLTAARSLL.QKQVRPMLLVDDRALPDFKGIQTSDPNAV
Retrocopy FVTNTTKESKQDLLQRLRKLEFDISENEIFTSLTAARSLLKQKQVRPMLLVDDRALPDFKGIQTSDPNAV

Parental  VIGLAPEHFHYQILNQAFRLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKATVVGKPEKT
          VIGL.PEHFHYQILNQAF.LLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKATVV.KPE.T
Retrocopy VIGLSPEHFHYQILNQAFWLLLDGAPLIAIHKARYYKRKDGLALGPGPFVTALEYATDTKATVVEKPE-T

Parental  FFLEALRGTGCEPEEAVMIGDDCRDDVGGAQDVGMLGILVKTGKYRASDEEKINPPPYLTCESFPHAVDH
          FFLEALRGTGCEPEEAVMIGDDCRDDVGGAQDVGMLGILVKTGKY.ASDEEKINPPPYLT.ESFPHAVDH
Retrocopy FFLEALRGTGCEPEEAVMIGDDCRDDVGGAQDVGMLGILVKTGKY*ASDEEKINPPPYLTYESFPHAVDH

Parental  ILQHLL
          ILQHLL
Retrocopy ILQHLL

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	2.02 RPM	45.16 RPM
SRP007412_brain_prefrontal_cortex	2.30 RPM	36.25 RPM
SRP007412_cerebellum	0.97 RPM	30.29 RPM
SRP007412_heart	0.59 RPM	12.37 RPM
SRP007412_kidney	0.82 RPM	24.65 RPM
SRP007412_liver	0.40 RPM	7.76 RPM
SRP007412_testis	0.94 RPM	9.23 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_595 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_595 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_595 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011893	1 retrocopy	retro_btau_1336,
Choloepus hoffmanni	ENSCHOG00000009397	1 retrocopy	retro_chof_100,
Macaca mulatta	ENSMMUG00000010999	1 retrocopy	retro_mmul_595 ,
Ictidomys tridecemlineatus	ENSSTOG00000008527	1 retrocopy	retro_itri_55,