RetrogeneDB ID: retro_mmul_1379

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 19:51556736..51557095(+)
• Located in intron of: ENSMMUG00000022930

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5AL1
• Ensembl ID: ENSMMUG00000006206
• Aliases: None
• Description: eukaryotic translation initiation factor 5A-like 1 [Source:HGNC Symbol;Acc:17419]

Sequence

>retro_mmul_1379
GGCCTTACTTGTAAGATGGTCGAGATGTCTACTTGTAAGACTGGCAAGCACAGCCATGCCAAGGTCCAGCTGGTTGTCAC
TGACATCTTTACTAGGAAGAAATATAAAGATAATTGCCTATCAACTTATAATGTGGATGTCCCCAACATCAAAAGGAATG
ACTTCCAGCTGCTTGGCATCCAGGGTGGGTACCCCTCACTGCTCCAGGACATCAGGGAGGTGCAAGAGGACCTTCTTCTG
CCTGAGGAGACCTTGGCAAGGAGATCGAGCAAAAGTACAACTGTGGAGAAGGGCCCCTGATCACCGTGCTGTCTGCCATG
ACATAGGAGGCAGCTGTTGCAGTCAAGGCCATGGCAAAA

Alignment

ORF - retro_mmul_1379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.69 %
• Parental protein coverage: 65.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGIQDGYLSLLQD
          G..CK.VEMST.KTGKH.HAKV.LV..DIFT.KKY.D.C.ST.N.DVPNIKRNDFQL.GIQ.GY.SLLQD
Retrocopy GLTCKMVEMSTCKTGKHSHAKVQLVVTDIFTRKKYKDNCLSTYNVDVPNIKRNDFQLLGIQGGYPSLLQD

Parental  SGEVREDLRLPE-GDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIKAMAK
          ..EV.EDL.LPE.GDLGKEIEQKY.CGE..LITVLSAMT.EAAVA.KAMAK
Retrocopy IREVQEDLLLPE<GDLGKEIEQKYNCGEGPLITVLSAMT*EAAVAVKAMAK

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	52.55 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	87.50 RPM
SRP007412_cerebellum	0.13 RPM	57.02 RPM
SRP007412_heart	0.12 RPM	76.61 RPM
SRP007412_kidney	0.00 RPM	80.87 RPM
SRP007412_liver	0.08 RPM	149.23 RPM
SRP007412_testis	0.04 RPM	139.16 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1379 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1379 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2004
Gorilla gorilla	retro_ggor_1448
Pongo abelii	retro_pabe_1640

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132507	3 retrocopies	retro_hsap_1788, retro_hsap_2004, retro_hsap_9,
Gorilla gorilla	ENSGGOG00000012032	2 retrocopies	retro_ggor_1448, retro_ggor_159,
Macaca mulatta	ENSMMUG00000006206	1 retrocopy	retro_mmul_1379 ,
Macaca mulatta	ENSMMUG00000022880	1 retrocopy	retro_mmul_2222,
Monodelphis domestica	ENSMODG00000006652	2 retrocopies	retro_mdom_1641, retro_mdom_190,
Pongo abelii	ENSPPYG00000007907	1 retrocopy	retro_pabe_1468,
Rattus norvegicus	ENSRNOG00000016478	3 retrocopies	retro_rnor_1627, retro_rnor_1947, retro_rnor_671,