RetrogeneDB ID: retro_mmul_2337

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:50016466..50017140(-)
• Located in intron of: ENSMMUG00000013149

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSFL1C
• Ensembl ID: ENSMMUG00000015994
• Aliases: None
• Description: NSFL1 cofactor p47 [Source:RefSeq peptide;Acc:NP_001253592]

Sequence

>retro_mmul_2337
GAGACCAGTACACCAAGACCATTTGCAGGAGGTGGCTATGGCCTTGGGGCAGCACCAAAGGAAGAGTCTGCTTATGTGGC
AGGATAAAAGAGACAGCATTCCCACCAAGATGTTCATGTAGTACTGAAACTCTACAAGAGTGGATTCAGCCTGGATAATG
GAGAACTCAGAAGCTACCAAGACCCATCCGATGCCCAGTTTCTGGAGTCTATCCACAGAGGAGAGGTGCCAGCAGAGCTG
TGGAGGCTAGCTCACAGTGGACAGGCGAACTTGGATATGGAGGACCATCGGGATGAGGACTTTATGAAGTCCAAAGGAGC
CTTCACTGGTGAGGGTCAGAAACCGAGCAGCACTGCCCCCCAGGTGTTGAGTACCATCTCTCCAGTCCAACTGGCAGAAA
ATGAAGCCAAAGCCAGCTCTTCCATCTTAATCGTCAAATCAGAGACTACCACAAACATCCAAATTTGGCTTGCAGATGGT
GAGAGGCTGGTACAGAAATTTAACTACAGCCACAGATCAGCAACATCCAACTCTTTATTGTGGATGCCTGGCCAGCCACG
GCTGCCACCAGCTTTATCCTCACGACTACTTTCCCAAACAAAGAGCTGGTTGACGAGAGCTGGACCCTGAAGGAAGCCAA
CCTGCTCAATGCTGCCATCATGCAGCGGTGAACC

Alignment

ORF - retro_mmul_2337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.41 %
• Parental protein coverage: 61.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETSKPRPFAGGGYRLGAAPEEESAYVAGEKRQHSSQDVHVVLKLWKSGFSLDNGELRSYQDPSNAQFLES
          ETS.PRPFAGGGY.LGAAP.EESAYVAG.KRQHS.QDVHVVLKL.KSGFSLDNGELRSYQDPS.AQFLES
Retrocopy ETSTPRPFAGGGYGLGAAPKEESAYVAG*KRQHSHQDVHVVLKLYKSGFSLDNGELRSYQDPSDAQFLES

Parental  IRRGEVPAELRRLAHGGQVNLDMEDHRDEDFVKPKGAFKAFTGEGQKLGSTAPQVLSTSSPAQQAENEAK
          I.RGEVPAEL.RLAH.GQ.NLDMEDHRDEDF.K.KGAF...TGEGQK..STAPQVLST.SP.Q.AENEAK
Retrocopy IHRGEVPAELWRLAHSGQANLDMEDHRDEDFMKSKGAF---TGEGQKPSSTAPQVLSTISPVQLAENEAK

Parental  ASSSILIDESEPTTNIQIRLADGGRLVQKFNHSHR-ISDIRLFIVDARPAMAATSFILMTTFPNKELADE
          ASSSILI..SE.TTNIQI.LADG.RLVQKFN.SHR.IS.I.LFIVDA.PA.AATSFIL.TTFPNKEL.DE
Retrocopy ASSSILIVKSETTTNIQIWLADGERLVQKFNYSHR<ISNIQLFIVDAWPATAATSFILTTTFPNKELVDE

Parental  SQTLKEANLLNAVIVQRLT
          S.TLKEANLLNA.I.QR.T
Retrocopy SWTLKEANLLNAAIMQR*T

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	0.22 RPM	48.41 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	65.45 RPM
SRP007412_cerebellum	0.06 RPM	48.43 RPM
SRP007412_heart	0.12 RPM	42.57 RPM
SRP007412_kidney	0.23 RPM	40.73 RPM
SRP007412_liver	0.59 RPM	33.88 RPM
SRP007412_testis	0.15 RPM	50.21 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2337 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2337 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2337 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000088833	1 retrocopy	retro_hsap_4050,
Gorilla gorilla	ENSGGOG00000013539	1 retrocopy	retro_ggor_2718,
Macropus eugenii	ENSMEUG00000003940	2 retrocopies	retro_meug_1890, retro_meug_605,
Macaca mulatta	ENSMMUG00000006487	1 retrocopy	retro_mmul_2068,
Macaca mulatta	ENSMMUG00000015994	1 retrocopy	retro_mmul_2337 ,
Mus musculus	ENSMUSG00000027455	1 retrocopy	retro_mmus_2565,
Nomascus leucogenys	ENSNLEG00000009341	1 retrocopy	retro_nleu_2800,
Otolemur garnettii	ENSOGAG00000002630	2 retrocopies	retro_ogar_1144, retro_ogar_1609,
Pongo abelii	ENSPPYG00000010851	1 retrocopy	retro_pabe_3324,
Pan troglodytes	ENSPTRG00000013164	1 retrocopy	retro_ptro_2745,