RetrogeneDB ID: retro_mmul_2507

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:74760300..74760893(+)
• 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_2507
ATGTCTCTCATCTTTGAGTGAATCTACCATGGCTTCAGAATTGTGATCTAGTTTCTAAGACTCTACAAGAAATATAGAAA
ATTTGTATTCTTGGGTTTGGACAAAGCAGGCAAAACCACTCTTTTTCACATGCTCAAAGGTGACAGATTGGAACAACACA
TTCCAACACTACATCTGACATGACAAGGGCTAACAATTGCTGGAATGACTTTTACAACTTTTAATCTTGGTGGGCACGAG
CAAGCACATCGGTTTGGAAAAATTATTTCCCAGCAATTAATGGGATTTTCCTTCTGGTGGATTGTGTGGATCATTCTTGC
CTTGTGGAATTCAAATTTGAACTTAAAGCTTTAATGACTGATGAAACAGTATACAATGTGCCAATTCGTATTTTGGGAAA
CAAAATTGACAGAACAGATGAACTCAAGGAAGAAAAACTCTGTGAGATATCTAGGCTTTATAGACAGACCACAGGCAAGG
AGAATGTGACCCTGAAGAATTTGAATGCTTGCCCCATAGAAGTGCCTGTGTGCAGTGTGCTCAAGAGGCAAGATTATGGC
GAATGTTTCCACTGGTTCTCCCAGTATATTGAC

Alignment

ORF - retro_mmul_2507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSFIFDWIYSGFSSVLQFLGLYKKTGKLVFLGLDNAGKTTLLHMLKDDRLGQHVPTLHPTSEELTIAGMT
          MS.IF..IY.GF..V..FL.LYKK..K.VFLGLD.AGKTTL.HMLK.DRL.QH.PTLH.T...LTIAGMT
Retrocopy MSLIFE*IYHGFRIVI*FLRLYKKYRKFVFLGLDKAGKTTLFHMLKGDRLEQHIPTLHLT*QGLTIAGMT

Parental  FTTFDLGGHVQARR-VWKNYLPAINGIVFLVDCADHERLLESKEELDSLMTDETIANVPILILGNKIDRP
          FTTF.LGGH.QA.R.VWKNY.PAINGI..LVDC.DH..L.E.K.EL..LMTDET..NVPI.ILGNKIDR.
Retrocopy FTTFNLGGHEQAHR<VWKNYFPAINGIFLLVDCVDHSCLVEFKFELKALMTDETVYNVPIRILGNKIDRT

Parental  EAISEERLREMFGLYGQTTGKGSVSLKELNARPLEVFMCSVLKRQGYGEGFRWMAQYID
          ....EE.L.E...LY.QTTGK..V.LK.LNA.P.EV..CSVLKRQ.YGE.F.W..QYID
Retrocopy DELKEEKLCEISRLYRQTTGKENVTLKNLNACPIEVPVCSVLKRQDYGECFHWFSQYID

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	0.34 RPM	15.01 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	11.50 RPM
SRP007412_cerebellum	0.19 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	0.04 RPM	62.27 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2507 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2507 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2507 has 0 orthologous retrocopies within eutheria group .

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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,