RetrogeneDB ID: retro_mmul_2596

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:72608767..72609860(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000032418
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MMU.4936
• Ensembl ID: ENSMMUG00000000983
• Aliases: None
• Description: Fructose-bisphosphate aldolase [Source:UniProtKB/TrEMBL;Acc:F6SYL4]

Sequence

>retro_mmul_2596
ATGCCCTACCAATATCCAGCGCTGACCCCGGAGCAGAAGAAGGAGCTGTCTGACGTCGCTCACCGCATCGTGGCACCCGG
CAAGGGCATCCTGGCTGCAGATGAGTCCACTGGGAGCATTGCCAAAGAGGCTGCAGTCCATTGGCACCGAGAACACCGAG
GAGAACCGGCGCTTCTACCGCCAGCTGCTGCTGACAGCTGACGACCGTGTGAACCCCTGCATTGGGGGTGTCATCCTCTT
CCACGAGACACTCTACCAGAAGGCGGATAATGGTCGTCCCTTCCCCCAAGTTATAAAATCCAAGGGCGGTGTTGTGGGCA
TCAAGGTAGACAAGGGCGTGGTTCCCCTGGCAGGGACAAATGGCGAGACTACCACCCAAGGGTTGGATGGGCTGTCTGAG
CGCTGTGCCCAGTACAAGAAGGATGGAGCTGACTTCGCCAAGTGGCGTTGTGTGCTGAAAATTGGGGAACACACCCCCTC
AGCCCTCGCCATCATGGAAAATGCCAATGTCCTGGCCCGTTATGCCAGCATCTGCCAGCAGAATGGCATTGTGCCCATCG
TGGAGCCTGAGATCCTCCCTGATGGGGACCATGACTTGAAGCGCTGCCAGTATGTGACCAAGAAGGTGCTGGCTGCTGTC
TACAAGGCTCTGAGCGACCACCACATCTACCTGGAAGGCACCTTGCTGAAGCCCAATATGGTCACCCCAGGCCACGCTTG
CACCCAGAAGTTTTCTCATGAGGAGATTGCCATGGCGACCGTCACAGCGCTGCGCCGCACAGTTCCCCCGGCTGTCACTG
GGATCACCTTCCTGTCTGGAGGCCAGAGTGAGGAGGAGGCATCCATCAACCTCAATGCCATTAACAAGTGCCCCCTGCTG
AAGCCCTGGGCCCTGACCTTCTCTTATGGCCGAGCCCTGCAGGCCTCTGCCCTGAAGGCCTGGGGTGGGAAGAAGGAGAA
CCTGAAGGCTGCACAGGAGGAGTACGTCAAGCGAGCCCTGGCCAACAGCCTTGCCTGTCAAGGAAAGTACACCCCGAGCG
GTCATGCCGGAGCTGCTGCTAGCGAGTCCCTCTTCGTCTCTAACCACGCCTAT

Alignment

ORF - retro_mmul_2596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.9 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPYQYPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAK-RLQSIGTENTEENRRFYRQLLLTADDR
          MPYQYPALTPEQKKELSD.AHRIVAPGKGILAADESTGSIAK.RLQSIGTENTEENRRFYRQLLLTADDR
Retrocopy MPYQYPALTPEQKKELSDVAHRIVAPGKGILAADESTGSIAK>RLQSIGTENTEENRRFYRQLLLTADDR

Parental  VNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYK
          VNPCIGGVILFHETLYQKAD.GRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYK
Retrocopy VNPCIGGVILFHETLYQKADNGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYK

Parental  KDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKV
          KDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVT.KV
Retrocopy KDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTKKV

Parental  LAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKFSHEEIAMATVTALRRTVPPAVTGITFLSGGQSEEE
          LAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKFSHEEIAMATVTALRRTVPPAVTGITFLSGGQSEEE
Retrocopy LAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKFSHEEIAMATVTALRRTVPPAVTGITFLSGGQSEEE

Parental  ASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGHA
          ASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGHA
Retrocopy ASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGHA

Parental  GAAASESLFVSNHAY
          GAAASESLFVSNHAY
Retrocopy GAAASESLFVSNHAY

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	4.48 RPM	243.71 RPM
SRP007412_brain_prefrontal_cortex	12.93 RPM	1018.99 RPM
SRP007412_cerebellum	1.42 RPM	134.77 RPM
SRP007412_heart	8.19 RPM	461.84 RPM
SRP007412_kidney	3.40 RPM	145.19 RPM
SRP007412_liver	0.44 RPM	72.76 RPM
SRP007412_testis	0.72 RPM	123.63 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2596 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2596 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2596 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008221	2 retrocopies	retro_cfam_190, retro_cfam_631,
Callithrix jacchus	ENSCJAG00000006874	1 retrocopy	retro_cjac_1803,
Cavia porcellus	ENSCPOG00000007434	1 retrocopy	retro_cpor_951,
Echinops telfairi	ENSETEG00000019230	1 retrocopy	retro_etel_20,
Homo sapiens	ENSG00000149925	1 retrocopy	retro_hsap_740,
Gorilla gorilla	ENSGGOG00000013979	1 retrocopy	retro_ggor_621,
Myotis lucifugus	ENSMLUG00000011210	3 retrocopies	retro_mluc_1172, retro_mluc_2634, retro_mluc_808,
Macaca mulatta	ENSMMUG00000000983	1 retrocopy	retro_mmul_2596 ,
Monodelphis domestica	ENSMODG00000015696	4 retrocopies	retro_mdom_1236, retro_mdom_1356, retro_mdom_528, retro_mdom_96,
Mus musculus	ENSMUSG00000030695	3 retrocopies	retro_mmus_2160, retro_mmus_42, retro_mmus_90,
Nomascus leucogenys	ENSNLEG00000002152	1 retrocopy	retro_nleu_133,
Oryctolagus cuniculus	ENSOCUG00000006329	1 retrocopy	retro_ocun_1550,
Ochotona princeps	ENSOPRG00000009760	1 retrocopy	retro_opri_914,
Pongo abelii	ENSPPYG00000007244	1 retrocopy	retro_pabe_636,
Pan troglodytes	ENSPTRG00000007983	1 retrocopy	retro_ptro_526,
Rattus norvegicus	ENSRNOG00000023647	7 retrocopies	retro_rnor_1343, retro_rnor_1541, retro_rnor_1796, retro_rnor_1807, retro_rnor_226, retro_rnor_2791, retro_rnor_536,