RetrogeneDB ID: retro_mmul_2237

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:72923166..72923950(-)
• Located in intron of: ENSMMUG00000017381

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX2
• Ensembl ID: ENSMMUG00000022712
• Aliases: None
• Description: Y box binding protein 2 [Source:HGNC Symbol;Acc:17948]

Sequence

>retro_mmul_2237
CCCGCTGCGGGGACCCCCTTGGCGCCTGGCCCTCGCGCCCCCCACCCACCCTGCCCCCCAGACCCCCGCGCCCGGAGTCA
GGCGGACAAGCAGGTGCTGGCAACCCGAGTCCTGGGCACTGTCATGTGGTTCGACGTCCGGAATGGTTACGGATTCATCA
ACAGGCATGACACCAAAGAAGATGTTTTTGTTCACCAGACAGCTATTAAAAGAACCCCGGGAAGTTTCTGCGCAGCGTTG
GTGATGGGCGGACTGTGGAATTTGATGTCGTGGAAGGAGAAAAGGGCACAGAAGCCGCTAATGTAACCGGGCCTGGGGAG
GTGCCCGTGAAGGGCAGTCATTATGCCCCCAGCCAACGTAGGTTCCGCCGATTTGTCCCCCGGCCTCCCTCAGTTGCCCC
ACCACGCATGGTGGCAGAGATCCCTTCATGGGGGACAGAACCTAGCAGCGAAGGGGAGCGGGCTGAAGACTCTGGGCAGC
GGCCCAGACGACGGGGCCCCCCACCCTTCTACCGACGGCAGTTTGCGCGAGGCCCTCGGCCCCCCAACCAGCAGCAGCCT
ACAGAGGGCACTGACGGGGTAGAACCCAAAGAAGCCCATTGGAGGGGCACTAACAGCAGGGAGATGAGCGGGTCCCCCGA
CCCCAATTCCGGCCCAGGTACTGAAGGCCTTTCCGCCCCAGGCCGCCCCGGCAGCCTACCACGAAAGGTGGGGAAGGTGA
GACGAAGCCCAGCCAAGGGCCTGCTGATGGTTCCCGCCCTGAACTCTACTTCCACCGGAGACGG

Alignment

ORF - retro_mmul_2237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.03 %
• Parental protein coverage: 73.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLAPGPRTPGNPATAASGTPAPPARSQADKPVLAIRVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIK
          P.A..P..PG.............ARSQADK.VLA.RVLGTV.WF.VRNGYGFINR.DTKEDVFVHQTAIK
Retrocopy PAAGTPLAPGPRXXXXXXXXXXXARSQADKQVLATRVLGTVMWFDVRNGYGFINRHDTKEDVFVHQTAIK

Parental  RNNPRKF-LRSVGDGETVEFDVVEGEKGAEAANVTGPGGVPVKGSRYAPNRRRFRRFIPRPPSVVPPPMV
          R..P..F.LRSVGDG.TVEFDVVEGEKG.EAANVTGPG.VPVKGS.YAP..RRFRRF.PRPPSV.PP.MV
Retrocopy R-TPGSF<LRSVGDGRTVEFDVVEGEKGTEAANVTGPGEVPVKGSHYAPSQRRFRRFVPRPPSVAPPRMV

Parental  AEIPSGGTGPGSEGERAEDSGQRPRRRRPPPFFYRRRFVRGPRPPNQQQPIESTDGVEPKETAPLEGHQQ
          AEIPS.GT.P.SEGERAEDSGQRPRRR.PPP.FYRR.F.RGPRPPNQQQP.E.TDGVEPKE.A...G...
Retrocopy AEIPSWGTEPSSEGERAEDSGQRPRRRGPPP-FYRRQFARGPRPPNQQQPTEGTDGVEPKE-AHWRGTNS

Parental  QGDERVPPP-RFRPRYRRPFRPRPPQQPTTEGGDGETKPSQGPTDGSRPEPQRPRNR
          ......P.P..FRPRY.RPFRPRPP.QPTT.GG.GETKPSQGP.DGSRPE....R.R
Retrocopy REMSGSPDP<QFRPRY*RPFRPRPPRQPTTKGGEGETKPSQGPADGSRPELYFHRRR

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	0.11 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	0.08 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.18 RPM	0.65 RPM
SRP007412_kidney	0.00 RPM	2.11 RPM
SRP007412_liver	0.00 RPM	0.51 RPM
SRP007412_testis	0.19 RPM	779.12 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2237 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2237 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2237 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016581	1 retrocopy	retro_cjac_1473,
Homo sapiens	ENSG00000006047	1 retrocopy	retro_hsap_637,
Macaca mulatta	ENSMMUG00000013136	5 retrocopies	retro_mmul_1139, retro_mmul_1423, retro_mmul_2017, retro_mmul_423, retro_mmul_861,
Macaca mulatta	ENSMMUG00000022712	1 retrocopy	retro_mmul_2237 ,
Nomascus leucogenys	ENSNLEG00000008063	1 retrocopy	retro_nleu_1954,
Oryctolagus cuniculus	ENSOCUG00000015064	1 retrocopy	retro_ocun_1762,
Pan troglodytes	ENSPTRG00000008673	3 retrocopies	retro_ptro_1264, retro_ptro_464, retro_ptro_50,