RetrogeneDB ID: retro_mmul_84

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:140008501..140008888(-)
• Located in intron of: ENSMMUG00000031522

Retrocopy information

• Ensembl ID: ENSMMUG00000006137
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KHDC1
• Ensembl ID: ENSMMUG00000018573
• Aliases: None
• Description: KH homology domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001244837]

Sequence

>retro_mmul_84
ATGGACATGGGAACAGGTGCTCTCAGCAAGGAGCCGTGGTGGACCCTACCCGAAAACTTTCATGCTCCAATTGTGTTCCA
CATGGAAGAGGACCAGGAGGAGCTCATATTCGGACTTGATGACACATACCTTCGCTGCATTGAGCTGCACAGCCACACCC
TTATTCAACTGGAGAGTTGTTTTACAGCTACAGGCCAGACTCGTGTGACCGTAGTCGGACCACCAATGGCAAAGCAGTGG
CTGCTGCTCATGTTCCGTTCCGTGGGGAGCCACTACTCCAAGTGTCACGCTCAAGGTCTGAAGATGCTCGAGCGTGTCCG
AAGCCGGCCCCTGACCAACGACGACCTGGTCGCCTCCATTAGCCTGCCACCCTACACCGGAGACTGA

Alignment

ORF - retro_mmul_84 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.03 %
• Parental protein coverage: 78.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDMGTSALSKKPWWTLPENFHAPMVFHMEEDQEELIFGHGDTYLRCIEVHSHTLIQLESWFTATGQTRVT
          MDMGT.ALSK.PWWTLPENFHAP.VFHMEEDQEELIFG..DTYLRCIE.HSHTLIQLES.FTATGQTRVT
Retrocopy MDMGTGALSKEPWWTLPENFHAPIVFHMEEDQEELIFGLDDTYLRCIELHSHTLIQLESCFTATGQTRVT

Parental  VVGPHRARQWLLHMFCCVGSQDSYHHARGLEMLEQVRSQPLTNDDLVTSISVPPYTGD
          VVGP..A.QWLL.MF..VGS..S..HA.GL.MLE.VRS.PLTNDDLV.SIS.PPYTGD
Retrocopy VVGPPMAKQWLLLMFRSVGSHYSKCHAQGLKMLERVRSRPLTNDDLVASISLPPYTGD

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	4.59 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	11.11 RPM
SRP007412_cerebellum	0.00 RPM	4.58 RPM
SRP007412_heart	0.00 RPM	2.18 RPM
SRP007412_kidney	0.00 RPM	1.76 RPM
SRP007412_liver	0.00 RPM	0.24 RPM
SRP007412_testis	0.15 RPM	3.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_84 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_84 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_84 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000009236	4 retrocopies	retro_dord_249, retro_dord_47, retro_dord_607, retro_dord_82,
Microcebus murinus	ENSMICG00000006451	1 retrocopy	retro_mmur_647,
Macaca mulatta	ENSMMUG00000018573	1 retrocopy	retro_mmul_84 ,
Mus musculus	ENSMUSG00000067750	1 retrocopy	retro_mmus_464,
Oryctolagus cuniculus	ENSOCUG00000028154	1 retrocopy	retro_ocun_735,
Otolemur garnettii	ENSOGAG00000006102	1 retrocopy	retro_ogar_2275,