RetrogeneDB ID: retro_mmul_2086

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:64144253..64145925(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2734
• Ensembl ID: ENSMMUG00000005880
• Aliases: None
• Description: Glucose-6-phosphate isomerase [Source:UniProtKB/TrEMBL;Acc:F6TLQ6]

Sequence

>retro_mmul_2086
ATGGCCGCTCTCACCCGGGACCCCCAGTTCCAGAAGCTGCAGCAATGGTATCGCGAGCACGGCTCCGAGCTGAACCTGAG
CCGCCTCTTCGATGCCGACAAGGATCGCTTCAACCACTTCAGCCTGACCCTCAACATCAACCATGGGCATATCCTGCTGG
ATTACTCCAAGAACCTGGTGACGGAGGATGTGATGCGGTTGCTGGTGGACCTGCCAAGTCCAGGGGCGTGGAGGCCGCCC
GGGAGCGGATGTTCAATGGTGAGAAGATCAACTACACCGAGGGTCGAGCTGTGCTGCACGTGGCTCTTCGGAACCGGTCA
AACACACCCATCCTGGTAGATGGCAAGGATGTGATGCCAGAGGTCAACAAGGTTCTGGACAAGATGAAGTCTTTCTGCCA
GCGTGTCCGGAGCGTGACTGGAAGGGGTACACAGGCAAGACCTTCACGGACGTCATCAACATTGGCATTGGCGGCTCCCA
CCTGGGACCCCTCATGGTGACTGAAGCCCTTAAGCCATACTCTTCGGAAGGTCCCCGCGTCTGGTATGTCTCCAACATTG
ATGGAACTCACATTGCCAAAACCCTGACCCAGCTGAATCCCGAGTCCTCCCTGTTCATCATCGCCTCCAAGACCTTTACC
ACCCAGGAGACCATCACGAATGCGGAGACGGCGAAGGAGTGGTTTCTCCAGGCGGCCAAGGATCCTTCTGCAGTGGCGAA
GCACTTTGTTGCCCTGTCTACTAACACGACCAAAGTGAAGGAGTTTGGAATTGACCCTCAAAACATGTTCGAGTTCTGGG
ATTGGGTGGGAGGACGCTACTCGCTGTGGTCGGCCATCGGACTCTCCATTGCCCTGCACGTGGGTTTTGACAACTTCCAG
CAGCTGCTCTCGGGGGGTCACTGGATGGACCAGCACTTCCGCACGACGCCCCTGGAGAAGAATGCCCCTGTCCTGCTGGC
CCTGCTGGGTATCTGGTACATCAACTGCTTTGGGTGTGAAACGCATGCCATGCTGCCCTATGACCAGTACCTGCACCGCT
TTGCTGCGTACTTCCAGCAGGGCGACATGGAGTCCAATGGGAAATACATCACCAAATCTGGCACCCGTGTGGACCACCAG
ACAGGCCCCATTGTGTGGGGGGAGCCTGGGACCAATGGCCAGCATGCTTTTTACCAGCTCATCCACCAAGGCACCAAGAT
GATACCCTGTGACTTCCTCATCCCGGTCCAGACCTAGCACCCCATAGGGAAGGGTTTGCATCACAAGATCCTCCTGGCCA
ACTTCCTGGCCCAGACGGAAGCCCTGATGAGGGGGAAATCAACGGAGGAGGCCCGAAAGGAGCTCCAGGCTGCAGGCAAG
AGTCCAGAGGACCTTGAGAGGCTGCTGCCACATAAGGTCTTTGAAGGCAATCACCCAACCAACTCTATTGTGTTCACCAA
GCTCACACCATTTATGCTTGGAGCCTTGGTCGCCATGTATGAGCACAAGATCTTTGTTCAGGGCATCATCTGGGACATCA
ACAGCTTTGACCAGTGGGGAGTGGAGCTGAAAAAGCAGCTGGCTAAGAAAATTGAGCCTGAGCTTGATGGCAGTGCTCAA
GTGACCTCTCACGATGCTTCCACCAACGGGCTTATCAACTTCATCAAGCAGCAGCGCGAGGCCAGAGTCCAA

Alignment

ORF - retro_mmul_2086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAALTRDPQFQKLQQWYREHGSELNLRRLFDADKDRFNHFSLTLNTNHGHILLDYSKNLVTEDVMRMLVD
          MAALTRDPQFQKLQQWYREHGSELNL.RLFDADKDRFNHFSLTLN.NHGHILLDYSKNLVTEDVMR.LVD
Retrocopy MAALTRDPQFQKLQQWYREHGSELNLSRLFDADKDRFNHFSLTLNINHGHILLDYSKNLVTEDVMRLLVD

Parental  L-AKSRGVEAARERMFNGEKINYTEGRAVLHVALRNRSNTPILVDGKDVMPEVNKVLDKMKSFCQRVRS-
          L.AKSRGVEAARERMFNGEKINYTEGRAVLHVALRNRSNTPILVDGKDVMPEVNKVLDKMKSFCQRVRS.
Retrocopy L<AKSRGVEAARERMFNGEKINYTEGRAVLHVALRNRSNTPILVDGKDVMPEVNKVLDKMKSFCQRVRS<

Parental  GDWKGYTGKTITDVINIGIGGSDLGPLMVTEALKPYSSEGPRVWYVSNIDGTHIAKTLTQLNPESSLFII
          .DWKGYTGKT.TDVINIGIGGS.LGPLMVTEALKPYSSEGPRVWYVSNIDGTHIAKTLTQLNPESSLFII
Retrocopy RDWKGYTGKTFTDVINIGIGGSHLGPLMVTEALKPYSSEGPRVWYVSNIDGTHIAKTLTQLNPESSLFII

Parental  ASKTFTTQETITNAETAKEWFLQAAKDPSAVAKHFVALSTNTTKVKEFGIDPQNMFEFWDWVGGRYSLWS
          ASKTFTTQETITNAETAKEWFLQAAKDPSAVAKHFVALSTNTTKVKEFGIDPQNMFEFWDWVGGRYSLWS
Retrocopy ASKTFTTQETITNAETAKEWFLQAAKDPSAVAKHFVALSTNTTKVKEFGIDPQNMFEFWDWVGGRYSLWS

Parental  AIGLSIALHVGFDNFEQLLSGAHWMDQHFRTTPLEKNAPVLLALLGIWYINCFGCETHAMLPYDQYLHRF
          AIGLSIALHVGFDNF.QLLSG.HWMDQHFRTTPLEKNAPVLLALLGIWYINCFGCETHAMLPYDQYLHRF
Retrocopy AIGLSIALHVGFDNFQQLLSGGHWMDQHFRTTPLEKNAPVLLALLGIWYINCFGCETHAMLPYDQYLHRF

Parental  AAYFQQGDMESNGKYITKSGTRVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRK
          AAYFQQGDMESNGKYITKSGTRVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQT.HPI.K
Retrocopy AAYFQQGDMESNGKYITKSGTRVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQT*HPIGK

Parental  GLHHKILLANFLAQTEALMRGKSTDEARKELQAAGKSPEDLERLLPHKVFEGNRPTNSIVFTKLTPFMLG
          GLHHKILLANFLAQTEALMRGKST.EARKELQAAGKSPEDLERLLPHKVFEGN.PTNSIVFTKLTPFMLG
Retrocopy GLHHKILLANFLAQTEALMRGKSTEEARKELQAAGKSPEDLERLLPHKVFEGNHPTNSIVFTKLTPFMLG

Parental  ALVAMYEHKIFVQGIIWDINSFDQWGVELGKQLAKKIEPELDGSAQVTSHDASTNGLINFIKQQREARVQ
          ALVAMYEHKIFVQGIIWDINSFDQWGVEL.KQLAKKIEPELDGSAQVTSHDASTNGLINFIKQQREARVQ
Retrocopy ALVAMYEHKIFVQGIIWDINSFDQWGVELKKQLAKKIEPELDGSAQVTSHDASTNGLINFIKQQREARVQ

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	0.78 RPM	257.27 RPM
SRP007412_brain_prefrontal_cortex	6.27 RPM	538.02 RPM
SRP007412_cerebellum	3.16 RPM	213.03 RPM
SRP007412_heart	2.00 RPM	237.49 RPM
SRP007412_kidney	0.94 RPM	221.36 RPM
SRP007412_liver	0.67 RPM	115.62 RPM
SRP007412_testis	3.66 RPM	167.36 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2086 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2086 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2086 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007303	3 retrocopies	retro_cfam_1715, retro_cfam_1935, retro_cfam_2101,
Cavia porcellus	ENSCPOG00000008562	1 retrocopy	retro_cpor_983,
Macropus eugenii	ENSMEUG00000010190	4 retrocopies	retro_meug_1022, retro_meug_1281, retro_meug_559, retro_meug_991,
Microcebus murinus	ENSMICG00000011620	1 retrocopy	retro_mmur_1496,
Myotis lucifugus	ENSMLUG00000003037	1 retrocopy	retro_mluc_444,
Macaca mulatta	ENSMMUG00000005880	1 retrocopy	retro_mmul_2086 ,
Mustela putorius furo	ENSMPUG00000007520	1 retrocopy	retro_mputfur_1370,
Mus musculus	ENSMUSG00000036427	1 retrocopy	retro_mmus_237,