RetrogeneDB ID: retro_mmul_785

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:7921133..7921637(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLTA
• Ensembl ID: ENSMMUG00000006132
• Aliases: None
• Description: None

Sequence

>retro_mmul_785
GACGAGGACTTCACCATCCTGGACGGTGGTGCCCCCAGGCCCCAGCCACATGGCAAGCTGCCTGGGGGTCCAGATGCTCG
ATGGAGTAATGAATGGCAAATACTACCAGGAAGGTAATGATCCAACAGACAGTTGTGCAGTATTTCACAAGTGGATAGAT
TGCAGTCAGAGCCTGAAAGTATCCATAAACGGAGAGAAAAGCAAACGGAACACTTGGAAGCCCTTGATGCCAATTCTCAG
GAGCACGAAGCAGAGTGGAAAGAAAAGGCAATAAAGAAGTTAGAGGTGTGATATGCAAGATAGGAGGAGCAGCTACAGAA
AATGAAAACAAACAGGGCAGCAGAAGAAGCCTTTGTAAATGACATTAACCAGTTGTTCCCAGGCACTGAGTAGGAATGTG
TGGCCTGTCTGTGTAACTTTAACCTCAAGTCCAGAAAGCAGGCCAAAGACATCTCACACAGGCACTCAGTCCTCATCTCC
CTCAAGCAGGCCCTGCTGGTGCAC

Alignment

ORF - retro_mmul_785 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.59 %
• Parental protein coverage: 77.88 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DEAFAILDGGAPGPQPHGEPPGGPGE-SAVAFGARGLESNGPTDSYA-AISQVDRLQSEPESIRKWREEQ
          DE.F.ILDGGAP.PQPHG..PGGP.....V..G....E.N.PTDS.A..ISQVDRLQSEPESI.K.RE.Q
Retrocopy DEDFTILDGGAPRPQPHGKLPGGPDA>DGVMNGKYYQEGNDPTDSCA<SISQVDRLQSEPESIHKRREKQ

Parental  MERLEALDANSRKQEAEWKEKAIKELEEWYARQDEQLQKTKANNRAAEEAFVNDIDESSPGTEWERVARL
          .E.LEALDANS...EAEWKEKAIK.LE..YAR..EQLQK.K..NRAAEEAFVNDI....PGTE.E.VA.L
Retrocopy TEHLEALDANSQEHEAEWKEKAIKKLEV*YAR*EEQLQKMK-TNRAAEEAFVNDINQLFPGTE*ECVACL

Parental  CDFNPKSSKQAKDVSRMRSVLISLKQAPLVH
          C.FN.KS.KQAKD.S...SVLISLKQA.LVH
Retrocopy CNFNLKSRKQAKDISHRHSVLISLKQALLVH

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	69.58 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	74.49 RPM
SRP007412_cerebellum	0.00 RPM	62.12 RPM
SRP007412_heart	0.00 RPM	28.27 RPM
SRP007412_kidney	0.00 RPM	103.99 RPM
SRP007412_liver	0.00 RPM	38.28 RPM
SRP007412_testis	0.19 RPM	21.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_785 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_785 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_785 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_955

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001137	1 retrocopy	retro_btau_327,
Homo sapiens	ENSG00000122705	2 retrocopies	retro_hsap_4022, retro_hsap_955,
Macropus eugenii	ENSMEUG00000010858	1 retrocopy	retro_meug_480,
Macaca mulatta	ENSMMUG00000006132	2 retrocopies	retro_mmul_2319, retro_mmul_785 ,
Monodelphis domestica	ENSMODG00000002610	1 retrocopy	retro_mdom_1148,
Nomascus leucogenys	ENSNLEG00000003874	1 retrocopy	retro_nleu_659,
Pongo abelii	ENSPPYG00000019069	1 retrocopy	retro_pabe_3300,
Pan troglodytes	ENSPTRG00000020930	1 retrocopy	retro_ptro_2727,