RetrogeneDB ID: retro_mmul_485

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:43978995..43979902(-)
• Located in intron of: ENSMMUG00000017104

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A1
• Ensembl ID: ENSMMUG00000005431
• Aliases: None
• Description: tricarboxylate transport protein, mitochondrial [Source:RefSeq peptide;Acc:NP_001253635]

Sequence

>retro_mmul_485
CGTGCTCTGGTGGCCCCTGAGCCTGTGTCCGGGAAGGCCAAACTGACACACCCAGGGGAGGCGATCCTGGCAGTTGGCCT
GGCGGGCGGCATTGACATCTGCATCACCTTCCCCACCAATACGTGAAGACGCAGCTGCATTTGGATGAACACTTGCACCT
GCCACAGTACCGGGGCACTGGGGACTGCGTGCAGCAGATGGTCCACAGCCATGGTGCCCTGGGCCTATACTGTGGCCTCA
GCTCCCACCTCTGCAGCTCCATCCCCAAGGCAGCCGTCAGGTTTGGAATGTTTGCGTTCCTCAGCAACCACATGCAGGAT
GCCCAGGGACAGCTGGACAGCACGCACGAGCTGCTCTGTGGCCCAGGAGCCAGCATGGCCAGGGGCCATGGAAGTCGTGT
GCCCCACGGAGACCATCAAGGTGAAGTTCAACCACAACCAGACCTCCCCAAACCCCAAGTACACAGGATTCTTCCATGCG
GTTAGGGAGATTGTGTGGGAACAAGGGCTGAAGGGAACGTACCAGGACCTCACAGCCACCATGCTGAAGCAGGGCTCGAA
CCAGGCTATCTGCTTCTTTGTCATGATCTCCCTGTGCAACTGGTACCGAGGGAACAACCTCAACAAGCCCATGAACCTGC
TGATCACTGGGGTCTTCAGAGCTATTGTGGGTGCAGCCAGTGTCTTTGGAAACACTCCTCTGGACGTGATTAAGACCCAG
ATGCAGGGCCTGGAGGTGCACAAATACTGGAACACATGGGACTGTGTCTTGCAGATCCTGAGGAAGGAGGGCTCAAGGCA
TTCTACAAGGGCACTGTTCCTGCCTGGGCTGGGTTGTCCTGAATGTGGCCATAGTGTTTATCATCTATGATGAGGTGGTA
AAACTGCTCAACAAAGTGTGGAAGACA

Alignment

ORF - retro_mmul_485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.13 %
• Parental protein coverage: 97.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RALAAAAPASGKAKLTHPGKAILAGGLAGGIEICITFPT-EYVKTQLQLDERSHPPRYRGIGDCVRQTVR
          RAL.A..P.SGKAKLTHPG.AILA.GLAGGI.ICITFPT..YVKTQL.LDE..H.P.YRG.GDCV.Q.V.
Retrocopy RALVAPEPVSGKAKLTHPGEAILAVGLAGGIDICITFPT<QYVKTQLHLDEHLHLPQYRGTGDCVQQMVH

Parental  SHGVLGLYRGLSSLLYGSIPKAAVRFGMFEFLSNHMRDAQGRLDSTRGLLCGLGAGVAE-AVVVVCPMET
          SHG.LGLY.GLSS.L..SIPKAAVRFGMF.FLSNHM.DAQG.LDST..LLCG.GA..A..A..VVCP.ET
Retrocopy SHGALGLYCGLSSHLCSSIPKAAVRFGMFAFLSNHMQDAQGQLDSTHELLCGPGASMAR>AMEVVCPTET

Parental  IKVKFIHDQTSPNPKYRGFFHGVREIVREQGLKGTYQGLTATVLKQGSNQAIRFFVMTSLRNWYRGDNPN
          IKVKF.H.QTSPNPKY.GFFH.VREIV.EQGLKGTYQ.LTAT.LKQGSNQAI.FFVM.SL.NWYRG.N.N
Retrocopy IKVKFNHNQTSPNPKYTGFFHAVREIVWEQGLKGTYQDLTATMLKQGSNQAICFFVMISLCNWYRGNNLN

Parental  KPMNPLITGVFGAIAGAASVFGNTPLDVIKTRMQGLEAHKYRNTWDCGLQILRKE-GLKAFYKGTVPR-L
          KPMN.LITGVF.AI.GAASVFGNTPLDVIKT.MQGLE.HKY.NTWDC.LQILRKE.GLKAFYKGTVP..L
Retrocopy KPMNLLITGVFRAIVGAASVFGNTPLDVIKTQMQGLEVHKYWNTWDCVLQILRKE<GLKAFYKGTVPA<L

Parental  GRVCLDVAIVFIIYDEVVKLLNKVWKT
          G.V.L.VAIVFIIYDEVVKLLNKVWKT
Retrocopy GWVVLNVAIVFIIYDEVVKLLNKVWKT

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	9.64 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	28.72 RPM
SRP007412_cerebellum	0.13 RPM	11.75 RPM
SRP007412_heart	0.24 RPM	15.43 RPM
SRP007412_kidney	0.59 RPM	170.89 RPM
SRP007412_liver	0.08 RPM	328.07 RPM
SRP007412_testis	0.11 RPM	32.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_485 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_485 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_485 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_334

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100075	2 retrocopies	retro_hsap_1632, retro_hsap_804,
Gorilla gorilla	ENSGGOG00000006198	2 retrocopies	retro_ggor_1230, retro_ggor_661,
Macaca mulatta	ENSMMUG00000005431	4 retrocopies	retro_mmul_1077, retro_mmul_1556, retro_mmul_1683, retro_mmul_485 ,
Nomascus leucogenys	ENSNLEG00000005215	2 retrocopies	retro_nleu_2866, retro_nleu_408,
Ochotona princeps	ENSOPRG00000011649	1 retrocopy	retro_opri_1053,
Pongo abelii	ENSPPYG00000029785	9 retrocopies	retro_pabe_1346, retro_pabe_1414, retro_pabe_1529, retro_pabe_1671, retro_pabe_3125, retro_pabe_3217, retro_pabe_334, retro_pabe_3564, retro_pabe_719,
Pan troglodytes	ENSPTRG00000014057	3 retrocopies	retro_ptro_1139, retro_ptro_1364, retro_ptro_560,
Tursiops truncatus	ENSTTRG00000006845	1 retrocopy	retro_ttru_228,