RetrogeneDB ID: retro_mmul_1795

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:135303490..135304307(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000004166
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EEF1D
• Ensembl ID: ENSMMUG00000001645
• Aliases: None
• Description: None

Sequence

>retro_mmul_1795
TCATCTCTGGCAGCCGCATCGTTGGTTGGAGTCAGAAAAATAGCTACAAACTTCCTAGTACATGAGAAGATCTGGCTCGA
CCAATTCAAATATGAAGATGCAGAAAGGAAATTCTACGAGCAGATGAATGGGCCTGTGGCCAGCACCTCCCGCCAGAGCT
CGGCCTCAGGGCCTCCAGCGGCTCCAGTGGAGACCACAGCGAGCTCTTCCTTCAGATCGCCAGCCTGAAAGTGGAGAATC
AGAGCCTGTGCGGCGTGGTGCAGGAGCTGCAGAGGGCCATCTCCAAGCTGGAGGCCCGGCTGAACGTGCTGGAGAAGACA
GACGAGCTCGCCCGGCCACGGTCCACAGCCCCGCAGACCCAGCACGTGTCTTCCATGCACCAAGTGGAGCTCTCCCCGCC
CCCCACTACACCCCAGGCCAGGCAGCAGAAGATAACGAGAATGATGACATTGATCTGTTGGCAGCGACAATAAGGAGGAA
GACAAGGAGGCAAGGCGGCTGTGGGAGGAGCGGCTGCGGCAGTACACCAAGAAGGCAAAGAATCCCTCGCTGGTGGCCAA
GTCCTCCATCCTGCTGGACATCAAGCGTTGGGACAATGAGACGGACATGACCCAGGTGGAGGCATGCGTGCGCTCCATTC
AAGCTGGATGGGCTGGTGAGCCGGGCCTCCAAGCTGGTGCCCGTGGGCTACGGTATCCGGAAGCTGCATATTCAGTGTGT
GGTGGAGGACAAGGTGGGGACAGACTTGCTGGAGGAGGAGATCACCAAGTTTGAGGAGCATGTGCAGAGTGTCGACATCG
CAGCTTTCAACAAGATC

Alignment

ORF - retro_mmul_1795 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.99 %
• Parental protein coverage: 94.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SGLSVSSLRPNRKMATNFLVHEKIWFDKFKYDDAERRFYEQMNGPVAGASRQTSGPG-ASSGPSGDHSEL
          S.L...SL...RK.ATNFLVHEKIW.D.FKY.DAER.FYEQMNGPVA..SRQ.S..G.ASSG.SGDHSEL
Retrocopy SSLAAASLVGVRKIATNFLVHEKIWLDQFKYEDAERKFYEQMNGPVASTSRQSSASG<ASSGSSGDHSEL

Parental  VVRIASLEVENQSLRGVVQELQQAISKLEARLNVLEKSS--PGHRATAPQTQHVSPMRQVE---PPAK-K
          ...IASL.VENQSL.GVVQELQ.AISKLEARLNVLEK.......R.TAPQTQHVS.M.QVE...PP....
Retrocopy FLQIASLKVENQSLCGVVQELQRAISKLEARLNVLEKTDELARPRSTAPQTQHVSSMHQVELSPPPTT<T

Parental  PATPAEDDEDDDIDLF-GSDNEEEDKEAAQLREERLRQYAEKKAKKPALVAKSSILLDVKPWDDETDMAQ
          P...AED.E.DDIDL..GSDN.EEDKEA..L.EERLRQY..KKAK.P.LVAKSSILLD.K.WD.ETDM.Q
Retrocopy PGQAAEDNENDDIDLL<GSDNKEEDKEARRLWEERLRQYT-KKAKNPSLVAKSSILLDIKRWDNETDMTQ

Parental  LEACVRSIQ-LDGLVWGASKLVPVGYGIRKLQIQCVVEDDKVGTDLLEEEITKFEEHVQSVDIAAFNKI
          .EACVRSIQ.LDGLV..ASKLVPVGYGIRKL.IQCVVE.DKVGTDLLEEEITKFEEHVQSVDIAAFNKI
Retrocopy VEACVRSIQ>LDGLVSRASKLVPVGYGIRKLHIQCVVE-DKVGTDLLEEEITKFEEHVQSVDIAAFNKI

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	17.93 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	56.40 RPM
SRP007412_cerebellum	0.00 RPM	19.37 RPM
SRP007412_heart	2.12 RPM	101.28 RPM
SRP007412_kidney	0.12 RPM	52.11 RPM
SRP007412_liver	0.04 RPM	113.76 RPM
SRP007412_testis	0.04 RPM	109.50 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1795 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1795 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1795 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000008109	1 retrocopy	retro_drer_26,
Macaca mulatta	ENSMMUG00000001054	6 retrocopies	retro_mmul_1456, retro_mmul_1767, retro_mmul_1881, retro_mmul_2140, retro_mmul_894, retro_mmul_969,
Macaca mulatta	ENSMMUG00000001645	4 retrocopies	retro_mmul_1795 , retro_mmul_197, retro_mmul_733, retro_mmul_747,