RetrogeneDB ID: retro_mmul_1760

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:38405030..38406185(+)
• Located in intron of: ENSMMUG00000001634

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2928
• Ensembl ID: ENSMMUG00000002863
• Aliases: None
• Description: protein TFG [Source:RefSeq peptide;Acc:NP_001244729]

Sequence

>retro_mmul_1760
ATGAATGGACAGTTGAACCTAAGTGGGAAGCTAATCATGAAAGCTCAACTTGGGGAGGATATTCCACAAATTCCTATCCA
TAATGAAGATATTAATATTACTTACGATGAATTAGTGCTAATGATGCAACGAGTTTTCAGGGGAAAGTTTCTGAGCAATG
TCGAAGTAACAATAAAGTACAATGATAAAGATGATGATCTTATAACAATTTTTGATAGTTCTGACCTTTCCTTTGCAATT
CAGTGTAGTAGGACACTGAAACTGACATTATTTGTTAATGGTCAACCAAGACCCCCTTGAATCAAGTCAGGTGAAATATC
TCTGTCGAGAACTGACAGAACTTTGAAATAAAGTGAATCATTTATTGGATAGCTTGGAATCACCTGGAGAACCAGGACCT
TCCACCAGTATTCCTGAAAATGATACTGTGGATGATAGGGAAGAAAAGCCTGCTTCTTTGGATTCTTCTGGAAAACAGTA
TATTCAGGTTATGGCAGCAAGTATGTCTGTTTTTGACCCTTTAAAAAAACCAAGATGAAATAAAAAATAATGTTACGTCG
GCGTCTGGCTTAACAGATGATCAGGTTTCAGGGCAACCCAGTGCTCTTGTAGAAGACTGTTCAGGAACACCTGACAGCAT
TGCCGCCGCCTCCTCAGCAGCAGCTCACCCACCAGGAGTTCAGCCACAGCAACCACCACATGCAGAAGCTAAAATACAAG
CAGGTCAGACTGAAAGTCAGCTGTACCAACAGTACCAGCAACAGGCTGGCTATGGTCACAGCGGCTACAGGCTCCACCTC
AGCAGCCTCAACAGTATGGGATTCAGTATTCAACAAGCCAGAGTCAGCAGAATGGACCCTAAACAACCTCAGCAGTTCCA
AGGATATGGCCAACAACCAACCACCTAGGCACCAGCTCCTGCCTTTCTGGTCAGCCTCAACAACTGCCTGCTCAGCCGCC
ACACAGTACCAGGCAAGCAATTATCCTGCACAAACTTCCCAAACTTCTCAGCCTACTAATTACACTGTGGCCCCCGCCTC
TCAACCTAGAATGGCTCCAAGCCAACCTGGGGCCTGAGCCTATCAACCAAGACCAGGTTTTACTTCACTTCCTGTAAGTA
GCATGACCCTTCCTCCAAGTGGGCCTAATCCTTAT

Alignment

ORF - retro_mmul_1760 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.95 %
• Parental protein coverage: 95.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MNGQLDLSGKLIIKAQLGEDIRRIPIHNEDI--TYDELVLMMQRVFRGKLLSNDEVTIKYKDEDGDLITI
          MNGQL.LSGKLI.KAQLGEDI..IPIHNEDI..TYDELVLMMQRVFRGK.LSN.EVTIKY.D.D.DLITI
Retrocopy MNGQLNLSGKLIMKAQLGEDIPQIPIHNEDINITYDELVLMMQRVFRGKFLSNVEVTIKYNDKDDDLITI

Parental  FDSSDLSFAIQCSRILKLTLFVNGQPR-PLESSQVKYLRRELIELRNKVNRLLDSLEPPGEPGPSTNIPE
          FDSSDLSFAIQCSR.LKLTLFVNGQPR.PLESSQVKYL.REL.EL.NKVN.LLDSLE.PGEPGPST.IPE
Retrocopy FDSSDLSFAIQCSRTLKLTLFVNGQPR>PLESSQVKYLCRELTEL*NKVNHLLDSLESPGEPGPSTSIPE

Parental  NDTVDGREEKPAS-DSSGKQSTQVMAASMSAFDPL-KNQDEINKNVMSAFGLTDDQVSGPPSAPAEDRSG
          NDTVD.REEKPAS.DSSGKQ..QVMAASMS.FDPL.KNQDEI..NV.SA.GLTDDQVSG.PSA..ED.SG
Retrocopy NDTVDDREEKPASLDSSGKQYIQVMAASMSVFDPL>KNQDEIKNNVTSASGLTDDQVSGQPSALVEDCSG

Parental  TPDSI-ASSSSAAHPPGVQPQQPPYTGAQTQAGQIEGQMYQQYQQQAGYG-AQQPQAPPQQPQQYGIQYS
          TPDSI.A.SS.AAHPPGVQPQQPP...A..QAGQ.E.Q.YQQYQQQAGYG..Q..QAPPQQPQQYGIQYS
Retrocopy TPDSIAAASSAAAHPPGVQPQQPPHAEAKIQAGQTESQLYQQYQQQAGYG<SQRLQAPPQQPQQYGIQYS

Parental  ASYSQQTG-PQQPQQFQGYGQQPTSQAPAPAF-SGQPQQLPAQPPQ-QYQASNYPAQTYTAQTSQPTNYT
          .S.SQQ.G.P.QPQQFQGYGQQPT..APAPAF.SGQPQQLPAQPP..QYQASNYPAQ..T.QTSQPTNYT
Retrocopy TSQSQQNG>PKQPQQFQGYGQQPTT*APAPAF<SGQPQQLPAQPPH<QYQASNYPAQ--TSQTSQPTNYT

Parental  VAPASQPGMAPSQPG--AYQPRPGFTSLPGSTMTPPPSGPNPY
          VAPASQP.MAPSQPG..AYQPRPGFTSLP.S.MT.PPSGPNPY
Retrocopy VAPASQPRMAPSQPGA*AYQPRPGFTSLPVSSMTLPPSGPNPY

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	0.11 RPM	47.73 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	42.60 RPM
SRP007412_cerebellum	0.00 RPM	56.76 RPM
SRP007412_heart	0.18 RPM	34.21 RPM
SRP007412_kidney	0.12 RPM	59.98 RPM
SRP007412_liver	0.00 RPM	68.16 RPM
SRP007412_testis	0.04 RPM	92.61 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1760 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1760 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1760 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3459
Pan troglodytes	retro_ptro_2345
Pongo abelii	retro_pabe_2860

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013928	1 retrocopy	retro_chof_406,
Homo sapiens	ENSG00000114354	1 retrocopy	retro_hsap_3459,
Macaca mulatta	ENSMMUG00000002863	1 retrocopy	retro_mmul_1760 ,
Nomascus leucogenys	ENSNLEG00000002849	1 retrocopy	retro_nleu_2712,
Ochotona princeps	ENSOPRG00000000781	3 retrocopies	retro_opri_34, retro_opri_849, retro_opri_958,
Pongo abelii	ENSPPYG00000013597	1 retrocopy	retro_pabe_2860,
Pan troglodytes	ENSPTRG00000015165	1 retrocopy	retro_ptro_2345,
Pteropus vampyrus	ENSPVAG00000017331	1 retrocopy	retro_pvam_1122,
Ictidomys tridecemlineatus	ENSSTOG00000025779	1 retrocopy	retro_itri_457,