RetrogeneDB ID: retro_mmul_2520

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:94260984..94261573(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3C6
• Ensembl ID: ENSMMUG00000012709
• Aliases: None
• Description: general transcription factor IIIC, polypeptide 6, alpha 35kDa [Source:HGNC Symbol;Acc:20872]

Sequence

>retro_mmul_2520
GAGAATGGAAAAGAGGAGGAATTGAAGGCAGAGATGTTGATTCCAGTAGAATTGTCAGGATTTTCTAAAAATGTGAAAAT
AAATGCAAGATTTGGAGAATTTACAATGAGAGGCCCATTCTGCAAGTGGACAGCTATCTCTTTGCTGGAGAGTACAAAGA
CCCTCTTCAGACCTATGCTATATTTCAAGAAAATGTTGAAAATGTAGATGCAGAAGGCAATAACAAAACAGTGCTAAAAT
ATAAATGCCATACAATGAAGCAGCTCAGCATGATAACTCTTCTGACAGACAAGAAGGAAGGAGAAGAGAACAGGTGGGGT
GGAATAGCTGATAATCAGGAAAATTTCTCCTATAGACCCAAAATGATTTGTAGCCTTCTACATAAAAATGAAGATGAAGA
AGTAGGTAGCTTCAACTCCAGACAAACTTTTGGAGGTGGAAGAGCAAGAGATTCAAACGGAAGATAGTTCAAACCTGACT
TATGAACAGGAGAAACCACTGCACTTGGAAATAGAGGTTTCTGGTTACGTTATTGATATCTCTTCTAAAACAGAAGGTTC
TGTTTTTATGGAAACTTAAAATGCTGCCT

Alignment

ORF - retro_mmul_2520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.2 %
• Parental protein coverage: 93.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEEEEEQLVLVELSGIIDSDFLS-KCQNKCKVLGIDTERPILQVDSCVFAGEYEDTLGTCVIFEENVEHA
          E...EE.L....L.....S.F...KC.NKCK...I..ERPILQVDS..FAGEY.D.L.T..IF.ENVE..
Retrocopy ENGKEEELKAEMLIPVELSGFSK<KCENKCKIWRIYNERPILQVDSYLFAGEYKDPLQTYAIFQENVENV

Parental  DTEGNNKTVLKYKCHTMKKLSMTRTLLTEKKEGEENIGGVEWLQIKDN--DFSYRPNMICSFLHENEDEE
          D.EGNNKTVLKYKCHTMK.LSM..TLLT.KKEGEEN.....W..I.DN...FSYRP.MICS.LH.NEDEE
Retrocopy DAEGNNKTVLKYKCHTMKQLSMI-TLLTDKKEGEEN----RWGGIADNQENFSYRPKMICSLLHKNEDEE

Parental  V-AASAPDKSLELEEEEIQMNDSSNLSCEQEKPMHLDIEDSGPLIDIPSETEGSVFMET-QMLP
          V..AS.PDK.LE.EE.EIQ..DSSNL..EQEKP.HL.IE.SG..IDI.S.TEGSVFMET..MLP
Retrocopy V>VASTPDKLLEVEEQEIQTEDSSNLTYEQEKPLHLEIEVSGYVIDISSKTEGSVFMET>KMLP

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	11.54 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.52 RPM
SRP007412_cerebellum	0.00 RPM	8.85 RPM
SRP007412_heart	0.00 RPM	19.67 RPM
SRP007412_kidney	0.00 RPM	45.42 RPM
SRP007412_liver	0.00 RPM	7.24 RPM
SRP007412_testis	0.00 RPM	45.65 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2520 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2520 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4728
Pan troglodytes	retro_ptro_3145

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003535	1 retrocopy	retro_amel_370,
Callithrix jacchus	ENSCJAG00000005248	2 retrocopies	retro_cjac_3118, retro_cjac_4098,
Dasypus novemcinctus	ENSDNOG00000014270	4 retrocopies	retro_dnov_1228, retro_dnov_1654, retro_dnov_377, retro_dnov_931,
Homo sapiens	ENSG00000155115	3 retrocopies	retro_hsap_3714, retro_hsap_4728, retro_hsap_4735,
Gorilla gorilla	ENSGGOG00000010681	1 retrocopy	retro_ggor_2511,
Myotis lucifugus	ENSMLUG00000013919	1 retrocopy	retro_mluc_897,
Macaca mulatta	ENSMMUG00000012709	3 retrocopies	retro_mmul_1700, retro_mmul_2520 , retro_mmul_2524,
Monodelphis domestica	ENSMODG00000017924	1 retrocopy	retro_mdom_876,
Mustela putorius furo	ENSMPUG00000010179	1 retrocopy	retro_mputfur_182,
Nomascus leucogenys	ENSNLEG00000012846	3 retrocopies	retro_nleu_1237, retro_nleu_2122, retro_nleu_2552,
Pan troglodytes	ENSPTRG00000018502	3 retrocopies	retro_ptro_2516, retro_ptro_3145, retro_ptro_3149,