RetrogeneDB ID: retro_mmul_2315

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:145408019..145408460(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.3016
• Ensembl ID: ENSMMUG00000006951
• Aliases: None
• Description: zinc finger HIT domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001247932]

Sequence

>retro_mmul_2315
GTCCACTCCCAGGACCCTGGGCAGCAGTGGGTGCTGGACTGGGCCACCTGGCAGTGTCGCATCAACTGGCAGCTGGAGAC
CCTGGAGAATGACAACTTCCAGGATGACCCCCATGTGGGACTCCCTCAGCTCGGCAAGAGACTGCCTCGGTTTGATGATG
ATGCGGATACCAGACGGTAAAAGAAGAAAACCTGAAGTGATCATTTTCAACTTTGCTTCCAAAAAATCTTTCAGGCCCTG
CTGGAGGAGCAGAACCTGAGTGTGGCCGAGGGCCCCAACTACCTGACAGCCTGTGCAGGGTCCCCATCGCAGCTGCAGTG
CTCCTTCTGCGCTGTCTGGCGTCTTCCCCTCTCCTACACCTGTGTCAGCTGTGGTGCCTGGTATTGCACCATGTGTTGTC
TGGGGACCCACCAGGAGACCAGATGTCTGAAGTGGACCATG

Alignment

ORF - retro_mmul_2315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.87 %
• Parental protein coverage: 95.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRSQDPGQRRVLDRAARQRRINRQLEALENDNFQDDPHAGLPQLGKRLPQFDDDADTGKKKKKTRGDHFK
          V.SQDPGQ..VLD.A..Q.RIN.QLE.LENDNFQDDPH.GLPQLGKRLP.FDDDADT...KKKT..DHF.
Retrocopy VHSQDPGQQWVLDWATWQCRINWQLETLENDNFQDDPHVGLPQLGKRLPRFDDDADTRR*KKKT*SDHFQ

Parental  LRFRKNFQALLEEQNLSVAEGPNYLTACAGPPSRPQRPFCAVCGFPSPYTCVSCGARYCTVRCLGTHQET
          L.F.K.FQALLEEQNLSVAEGPNYLTACAG.PS..Q..FCAV...P..YTCVSCGA.YCT..CLGTHQET
Retrocopy LCFQKIFQALLEEQNLSVAEGPNYLTACAGSPSQLQCSFCAVWRLPLSYTCVSCGAWYCTMCCLGTHQET

Parental  RCLKWTV
          RCLKWT.
Retrocopy RCLKWTM

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	6.95 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	25.70 RPM
SRP007412_cerebellum	0.00 RPM	6.26 RPM
SRP007412_heart	0.00 RPM	13.54 RPM
SRP007412_kidney	0.00 RPM	31.34 RPM
SRP007412_liver	0.00 RPM	58.07 RPM
SRP007412_testis	0.00 RPM	15.83 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2315 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2315 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2315 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000010174	1 retrocopy	retro_etel_1701,
Homo sapiens	ENSG00000106400	1 retrocopy	retro_hsap_4012,
Gorilla gorilla	ENSGGOG00000016713	1 retrocopy	retro_ggor_2694,
Macaca mulatta	ENSMMUG00000006951	1 retrocopy	retro_mmul_2315 ,
Pan troglodytes	ENSPTRG00000019525	1 retrocopy	retro_ptro_2723,
Rattus norvegicus	ENSRNOG00000001418	2 retrocopies	retro_rnor_2162, retro_rnor_2278,