RetrogeneDB ID: retro_mmul_483

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:43475511..43476032(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2F2
• Ensembl ID: ENSMMUG00000012634
• Aliases: None
• Description: general transcription factor IIF subunit 2 [Source:RefSeq peptide;Acc:NP_001253640]

Sequence

>retro_mmul_483
ATCAGCACACCCAGGGTGCCTCGGTTCCTTGTGCGTGGGCTCAGAGGGCAGATGCTCACAGCGTTGACTAAGCGTGCACC
AAGTAAGCTCTCATTGGAAGGAACTGTGGTACAGCGAGGGGAATGCCAACCAGCTGCAAATTAAAACTGCATGAGACTGA
AGAGAATGCAAACGCAGGAATCTGCCAAACCTGCCCAAACCCTACAGAAACCGGACAAGGTTGTCACAGTTGGTTATAAA
CCTGTTGCTAATCATCAGTATAATATTGCGTATGAGAAGAAAAAGAAAGAAGAGGGAAGGAAGGTGAAGGCTGATAAACA
CCACGTTTTATCCTTGCTATTTGCTGCTTCGAGAAACACCAGTATTACAACATAAAGGACATGGTCGGCATCACAGTGCA
ACCTATGTGTGCCTCGAAGAAATCTTGAATGATACGGGTGTTTGAAATGTTAGCAGACCCCACAAAAGCACATGGAGCTG
AAGGTAGAGACTGACATTATCCAGCAGCAGCCAAGAGTGAG

Alignment

ORF - retro_mmul_483 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.54 %
• Parental protein coverage: 70.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VSAPREHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAASENYMRLKRLQIEESSKPVRLSQQ
          .S.PR...F......GQ.LT..T.....KLSLEG.VVQR.EC.PAA..N.MRLKR.Q..ES.KP....Q.
Retrocopy ISTPRVPRFLVRGLRGQMLTALTKRAPSKLSLEGTVVQRGECQPAAN*NCMRLKRMQTQESAKPAQTLQK

Parental  LEKVVTTNYKPVANHQYNIEYERKKKEDGKRARADKQHVLDMLFSA-FEKHQYYNLKDLVDITKQPV-VY
          ..KVVT..YKPVANHQYNI.YE.KKKE.G....ADK.HVL..LF.A.FEKHQYYN.KD.V.IT.QP..V.
Retrocopy PDKVVTVGYKPVANHQYNIAYEKKKKEEGRKVKADKHHVLSLLFAA<FEKHQYYNIKDMVGITVQPM<VC

Parental  LKEILKEIGVQNVKGIHKNTW-ELKPEYR-HYQGEEKSD
          L.EIL...GV.NV...HK.TW.ELK.E...HY....KS.
Retrocopy LEEILNDTGV*NVSRPHKSTW<ELKVETD<HYPAAAKSE

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	5.83 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.82 RPM
SRP007412_cerebellum	0.00 RPM	3.36 RPM
SRP007412_heart	0.00 RPM	4.59 RPM
SRP007412_kidney	0.00 RPM	6.22 RPM
SRP007412_liver	0.00 RPM	6.25 RPM
SRP007412_testis	0.00 RPM	10.97 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_483 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_483 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_483 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_368
Pan troglodytes	retro_ptro_288
Gorilla gorilla	retro_ggor_379
Callithrix jacchus	retro_cjac_2990

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028333	1 retrocopy	retro_acar_174,
Choloepus hoffmanni	ENSCHOG00000007391	1 retrocopy	retro_chof_1718,
Callithrix jacchus	ENSCJAG00000019220	2 retrocopies	retro_cjac_1351, retro_cjac_2990,
Homo sapiens	ENSG00000188342	2 retrocopies	retro_hsap_2990, retro_hsap_368,
Gorilla gorilla	ENSGGOG00000006657	2 retrocopies	retro_ggor_2070, retro_ggor_379,
Myotis lucifugus	ENSMLUG00000010505	1 retrocopy	retro_mluc_58,
Macaca mulatta	ENSMMUG00000012634	2 retrocopies	retro_mmul_1913, retro_mmul_483 ,
Monodelphis domestica	ENSMODG00000025484	1 retrocopy	retro_mdom_231,
Nomascus leucogenys	ENSNLEG00000002097	1 retrocopy	retro_nleu_2440,
Nomascus leucogenys	ENSNLEG00000002106	1 retrocopy	retro_nleu_742,
Otolemur garnettii	ENSOGAG00000012517	1 retrocopy	retro_ogar_2772,
Procavia capensis	ENSPCAG00000005868	3 retrocopies	retro_pcap_102, retro_pcap_173, retro_pcap_375,
Pongo abelii	ENSPPYG00000005333	1 retrocopy	retro_pabe_93,
Pan troglodytes	ENSPTRG00000005840	3 retrocopies	retro_ptro_2022, retro_ptro_288, retro_ptro_2932,
Rattus norvegicus	ENSRNOG00000029316	1 retrocopy	retro_rnor_1288,
Ictidomys tridecemlineatus	ENSSTOG00000006891	1 retrocopy	retro_itri_19,