RetrogeneDB ID: retro_mmul_905

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:16506301..16507079(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBQLN4
• Ensembl ID: ENSMMUG00000009983
• Aliases: None
• Description: ubiquilin 4 [Source:HGNC Symbol;Acc:1237]

Sequence

>retro_mmul_905
AAGACAAAAATCTCCTGGAGGTTTAAGGGTCAGCAGGATCAGCTGATCCTGATCTTTGCAAACAAGGCCCTCAAGGATGG
GGACACACTGAACCAGCATGGGATCAAGGACAGGCTCACCAGCCATCTGTTCACCCAGACCCCTCAAAAGGCTCAAGATG
TGGCTGCTGCTACTGCTTCCTCCCCCTCAACTCCAGACCCTGCCTCAGAATCCTCCACCATGACTACCCACCATCCTGCA
AGTCCTGCACCTCTGGCTGTACCACTTCAGATGCTGGTGGTAGAAGCCAGAACAGCAGTGTGGAGGGAGGTGCCTTTTTA
GGGGTTGGGGAGGGGCCCTTTAGTGCTACCACATCCATACTCTCTGGCTTTTGGGGTATGCTGGGGCTCAGCGGCACGAC
TTGGGCTTTACCAACTTCATAGAGCTACAGCAGATGCAGAGGCAGCTGATGTCCAAACTTGAGATGCTGTTGCAGATCTT
AGAAAGCCTTCTGCTCCAGGACATGATGTCTATCCCTGGCCTGATGTGCCACAGATCATGGCCAATACCCAGATGCAGCA
ACTGATGGGGAAGAACCCCAAGATAAGCTACTATATTCCCCAACTCAAGTTTACGAGGCAGGTGATGGAGCTTGTTTGGA
ATCCAGCATAATGCAGGAGATAATGCAGAAGCAGACCAGGGCCTGAACAACTTTGAGAGTGCCCCCAGAGGCTGCAATGC
TCTCTACTGCATGTATACAGACATACAGGGGCCCACGTTTAGTGTTGAACAGGAACAA

Alignment

ORF - retro_mmul_905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.57 %
• Parental protein coverage: 51.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KEEISRRFKAQQDQLVLIFAGKILKDGDTLNQHGIKDGLTVHLVIKTPQKAQDPAAATASSPSTPDPASA
          K..IS.RFK.QQDQL.LIFA.K.LKDGDTLNQHGIKD.LT.HL...TPQKAQD.AAATASSPSTPDPAS.
Retrocopy KTKISWRFKGQQDQLILIFANKALKDGDTLNQHGIKDRLTSHLFTQTPQKAQDVAAATASSPSTPDPASE

Parental  PSTTPASPATPAQPS-TSGSASSDAGSGSRRSS-GGGPSPGAGEGPPSATASILSGFGGILGLGSL-GLG
          .ST.......PA.P..TSG...SDAG..S..SS..GG...G.GEGP.SAT.SILSGF.G.LGL.....LG
Retrocopy SSTMTTHH--PASPA<TSGCTTSDAGGRSQNSSVEGGAFLGVGEGPFSATTSILSGFWGMLGLSGT<DLG

Parental  SANFMELQQQMQRQLMSNPEMLSQIMENPLVQDMMSNPDLMRH-MIMANPQMQQLMERNPEISHMLNNPE
          ..NF.EL.QQMQRQLMS..EML.QI.E..L.QDMMS.P.LM.H..IMAN.QMQQLM..NP.IS.......
Retrocopy FTNFIEL-QQMQRQLMSKLEMLLQILESLLLQDMMSIPGLMCH<QIMANTQMQQLMGKNPKISYYIPQLK

Parental  LMRQTMELARNPA-MMQEMMRNQDRA-LSNLESIPGGYNALRRMYTDIQEPMFSAAREQ
          ..RQ.MEL..NPA..MQE.M..Q.RA.L.N.ES.P.G.NAL..MYTDIQ.P.FS...EQ
Retrocopy FTRQVMELVWNPA<IMQEIMQKQTRA<LNNFESAPRGCNALYCMYTDIQGPTFSVEQEQ

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	26.33 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	56.17 RPM
SRP007412_cerebellum	0.00 RPM	16.72 RPM
SRP007412_heart	0.00 RPM	8.42 RPM
SRP007412_kidney	0.00 RPM	9.51 RPM
SRP007412_liver	0.00 RPM	14.37 RPM
SRP007412_testis	0.04 RPM	7.92 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_905 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_905 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_905 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000160803	1 retrocopy	retro_hsap_2859,
Gorilla gorilla	ENSGGOG00000008916	1 retrocopy	retro_ggor_26,
Macropus eugenii	ENSMEUG00000016573	1 retrocopy	retro_meug_109,
Microcebus murinus	ENSMICG00000002222	1 retrocopy	retro_mmur_1146,
Macaca mulatta	ENSMMUG00000009983	1 retrocopy	retro_mmul_905 ,
Monodelphis domestica	ENSMODG00000016961	1 retrocopy	retro_mdom_530,
Pan troglodytes	ENSPTRG00000001444	1 retrocopy	retro_ptro_1934,