RetrogeneDB ID: retro_mmul_1747

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:6417774..6418302(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2426
• Ensembl ID: ENSMMUG00000001690
• Aliases: CNN3, calponin-3
• Description: calponin-3 [Source:RefSeq peptide;Acc:NP_001248738]

Sequence

>retro_mmul_1747
ACAACCATGGACATCAGGGTTAAATATGCAGAAAAACAAACAAGACATTAGGATGAAGGAAAATTAAAAGCTGTCAAAAC
TGTAATTGGATTGCAGATGGGAACCAACGAAGTGCCAGCCAGGCAGGTATGTCAACTTGTGGGACTACAGGCATCTTTAT
GATCCCAAAATGCAAACTGACAAACCTTTTGACCAGACCACAATTTGTCTGCAGATGGGCACTAACAAAGCAGACAGCCA
GATGGGGATGTCAGCACCAGGCACCAGAAGGGCCATCTACTATCAGAAGCTAACATTACAGCCAGTAGACCGCTTGACCA
TTTCTCTACAGATGGGTACCAACACGCTTCCCAGAAAAGAATGGGTGTGCATGGGCTTGGGGGGCAAGTATATGGTCGCA
AATACTGTGCTGCTTTATCATTCACAACAGAAACAAATGGTTTGAAAATCAGTGATAGTGATTATCACACAGAATATCCA
GATGACTAACATGGCGAGTACCAAGGTGACTGCCCTAGAGATTACCAA

Alignment

ORF - retro_mmul_1747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.33 %
• Parental protein coverage: 54.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TTIDIGVKYAEKQTRRFDEGKLKAGQSVIGLQMGTN-KCASQAGMTAYGTR-RHLYDPKMQTDKPFDQTT
          TT.DI.VKYAEKQTR..DEGKLKA...VIGLQMGTN...ASQAGM...GT..RHLYDPKMQTDKPFDQTT
Retrocopy TTMDIRVKYAEKQTRH*DEGKLKAVKTVIGLQMGTN<RSASQAGMSTCGTT<RHLYDPKMQTDKPFDQTT

Parental  ISLQMGTNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGL-GRQVYDPKY
          I.LQMGTNK..SQ.GM.APGTRR.IY.QKLTLQPVD..TISLQMGTN...........GL.G.QVY..KY
Retrocopy ICLQMGTNKADSQMGMSAPGTRRAIYYQKLTLQPVDRLTISLQMGTNTLPRKEWVCM-GL<GGQVYGRKY

Parental  CAAPTEPVIHNGSQGTGTNGSEISDSDYQAEYPDEYHGEYQ
          CAA.......NG..............D...EY.......YQ
Retrocopy CAALSFTTETNGLKISDSDYHTEYPDD*HGEYQGDCPRDYQ

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	70.26 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	48.87 RPM
SRP007412_cerebellum	0.00 RPM	79.75 RPM
SRP007412_heart	0.00 RPM	49.76 RPM
SRP007412_kidney	0.00 RPM	207.63 RPM
SRP007412_liver	0.00 RPM	71.81 RPM
SRP007412_testis	0.00 RPM	14.14 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1747 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1747 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1747 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016707	1 retrocopy	retro_amel_1412,
Bos taurus	ENSBTAG00000020345	1 retrocopy	retro_btau_1211,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Homo sapiens	ENSG00000117519	1 retrocopy	retro_hsap_3419,
Gorilla gorilla	ENSGGOG00000013870	1 retrocopy	retro_ggor_2312,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Macaca mulatta	ENSMMUG00000001690	1 retrocopy	retro_mmul_1747 ,
Macaca mulatta	ENSMMUG00000004705	1 retrocopy	retro_mmul_2328,
Macaca mulatta	ENSMMUG00000015306	1 retrocopy	retro_mmul_1131,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Mus musculus	ENSMUSG00000053931	2 retrocopies	retro_mmus_1052, retro_mmus_2544,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190, retro_vpac_449,