RetrogeneDB ID: retro_mmul_1825

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:28787693..28788282(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAR1B
• Ensembl ID: ENSMMUG00000004417
• Aliases: None
• Description: SAR1 homolog B [Source:RefSeq peptide;Acc:NP_001247957]

Sequence

>retro_mmul_1825
ATGTCTTTCATCTTTGAGTGGATCTACAATGGCTTCAGCAGTGTTCTCCAGTTCCTGGACTCCACAAGAAATTTGGAAAA
CTTGTATTCTTGGGTTTGGACAATGCAGGCAAAACCACTCTTCTTCGCATGCTCAAAGATGACAGATTGGGTCAACATGT
TCCAACACTACATCTGACATCAGAAAAGCTAATAATTGCTGGAATGACTTTTACAACTTTTGATCTTGGTGGACACAAGC
AACCATGTCAGGTTTGAAAAAATTATCTCCCAGGAATTAATGGGATTGTTTTTCTGGTGAACTCTGTAGATCATTCTGGC
CTCAGGGAATCCAAAGTTGAGCTTAATGCTTTAATGACTGATGAAATAATATCCAATGTGCCAATCCTTATCCTGGGTAA
CAAAATAGACAGAACAATGCAATCAGTGAAGAAAAACTCTTTGAGATATTTGGGCTTTCTGGATAGACCACAGGAAAGAG
GAACGTGGCCCTTTAGGAGCTGAACGCTCACCCCGTGGAAGTGTTCATGTGCAGCGTGCTCAAGAGGCAAGGCGAGGGCG
AGGGATTCTGCTGGCTCTCCCAATATATT

Alignment

ORF - retro_mmul_1825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.89 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSFIFDWIYSGFSSVLQFL-GLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGM
          MSFIF.WIY.GFSSVLQFL.GL.KK.GKLVFLGLDNAGKTTLL.MLKDDRLGQHVPTLH.TSE.L.IAGM
Retrocopy MSFIFEWIYNGFSSVLQFL<GLHKKFGKLVFLGLDNAGKTTLLRMLKDDRLGQHVPTLHLTSEKLIIAGM

Parental  TFTTFDLGGHVQARRVWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRP
          TFTTFDLGGH.Q...V.KNYLP.INGIVFLV...DH..L.ESK.EL..LMTDE.I.NVPILILGNKIDR.
Retrocopy TFTTFDLGGHKQPCQV*KNYLPGINGIVFLVNSVDHSGLRESKVELNALMTDEIISNVPILILGNKIDRT

Parental  -EAISEERLREMFGLYGQTTGKGSVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYI
          ..AISEE.L.E.FGL.G.TTGK..V.L.ELNA.P.EVFMCSVLKRQG.GEGF.W..QYI
Retrocopy <NAISEEKLFEIFGLSG*TTGKRNVAL*ELNAHPVEVFMCSVLKRQGEGEGFCWLSQYI

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	15.01 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	11.50 RPM
SRP007412_cerebellum	0.06 RPM	17.63 RPM
SRP007412_heart	0.00 RPM	20.37 RPM
SRP007412_kidney	0.00 RPM	23.47 RPM
SRP007412_liver	0.00 RPM	44.61 RPM
SRP007412_testis	3.02 RPM	62.27 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1825 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1825 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1825 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3568
Pan troglodytes	retro_ptro_2423
Pongo abelii	retro_pabe_2940

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013784	3 retrocopies	retro_dnov_1584, retro_dnov_1804, retro_dnov_919,
Equus caballus	ENSECAG00000012409	1 retrocopy	retro_ecab_948,
Loxodonta africana	ENSLAFG00000001021	1 retrocopy	retro_lafr_1043,
Macaca mulatta	ENSMMUG00000004417	3 retrocopies	retro_mmul_1825 , retro_mmul_2507, retro_mmul_304,