RetrogeneDB ID: retro_mmul_2135

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:23238983..23239862(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.17969
• Ensembl ID: ENSMMUG00000000056
• Aliases: None
• Description: 5-azacytidine-induced protein 2 [Source:RefSeq peptide;Acc:NP_001253904]

Sequence

>retro_mmul_2135
TATGAAGACATCAAAAAAGGACTTAAGGATTCAGAGAAAGAGAAGACTTATGTTAAAAAAAAGAATTAGATTTTTGGAAG
AAAAGCTTACAGGAGCTCAATTAGATGAAGAAATAAGTTTTGTGGAATAGCAACAAGTAAATAGGGCCTATTATGTATAT
TGAAACATTTGCATTGATAGAGATAATTTAGAGAACAAATCGAATAAAATGAGTAAACACAAGTCTGAATCTTTAAAAGT
ATTGAATGAACAGATGCAATCTAAAGAAGCAGAACTCTAGCTAAGGACAGAGGTGGAAACTCAGCTGGTGATGAAGAATT
TCAATCTACCTTCATCAAACTGGGAGGTGGAAAAGTTAAGCAGTGACCTGAAGATCCATGGTTTGGAACAAGAGTTGATG
AGGAAAGAATGTAATGATCTCAAAATAGAACCACTCAAAAACCAAACAAATCTCTGTATCAGGAAGACAATCTGAAGAGC
AGAGATCTCTGAAGAGTAAGAACTTCAACTGATAATACGTAGAATGCATACTGGCAACTGAGGAGATAAATGTCTAGTTT
ATATCTGGTGACTCAAGTGCTAGCTGAACTATTAAGAAAACTGAAAACCCCAACTTCAATCAAGACAGCCTGCACCTCAG
TAGGATGCATTGAAGACCCTTGCAAAGATGGCACAAAACTGCACATGATGAATTTTACTGCAACATACACAAGACATCCC
CTTCTCTCACCAAATGGCAAAGCTCTTTGTTATACTACATCTTCCTCTTTACCAGGAGATATAAAGGTTTTATCAGAGAA
AGCAGCCCTCCAATCACGGACAGATAATGAGAGAGCCATTCCTAATGAGGGCACACACTCTTATGGCAGAAATTCTCTG

Alignment

ORF - retro_mmul_2135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.64 %
• Parental protein coverage: 76.14 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YEDIKKRLKDSEKENS-LLKKRIRFLEEKLI-ARFDEETSSVGREQVNKAYHAYREVCIDRDNLKSKLDK
          YEDIKK.LKDSEKE........IRFLEEKL..A..DEE.S.V...QVN.AY..Y...CIDRDNL..K..K
Retrocopy YEDIKKGLKDSEKEKT>MXXXXIRFLEEKLTGAQLDEEISFVE*QQVNRAYYVY*NICIDRDNLENKSNK

Parental  MNKDNSESLKVLNEQLQSKEVELLQLRTEVETQQVMRNLNTPSSNWEVEKLSCDLKIHGLEQELELMRKE
          M.K..SESLKVLNEQ.QSKE.EL..LRTEVETQ.VM.N.N.PSSNWEVEKLS.DLKIHGLEQEL..MRKE
Retrocopy MSKHKSESLKVLNEQMQSKEAEL*-LRTEVETQLVMKNFNLPSSNWEVEKLSSDLKIHGLEQEL--MRKE

Parental  CSDLKIELQKAKQT-DPYQEDNLKSRDLQKLSISSDNMQHAYWELKREMSNLHLVTQVQAELLRKLKTST
          C.DLKIE..K.......YQEDNLKSRDL.....S.DN...AYW.L.R.MS.L.LVTQV.AELLRKLKT.T
Retrocopy CNDLKIEPLKNQTN<SLYQEDNLKSRDL*RVRTSTDNT*NAYWQLRR*MSSLYLVTQVLAELLRKLKTPT

Parental  AIKKACAPVGCSEDLGRDSTKLHLMNFTATYTRHPPLSPNGKALCHAASSPLPGDIKVLSEKAVLQSWTD
          .IK.AC..VGC.ED...D.TKLH.MNFTATYTRHP.LSPNGKALC...SS.LPGDIKVLSEKA.LQS.TD
Retrocopy SIKTACTSVGCIEDPCKDGTKLHMMNFTATYTRHPLLSPNGKALCYTTSSSLPGDIKVLSEKAALQSRTD

Parental  NERSIPNDGTCFQEHSSYGRNSL
          NER.IPN.GT....HS.YGRNSL
Retrocopy NERAIPNEGT----HS-YGRNSL

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	21.07 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	10.15 RPM
SRP007412_cerebellum	0.00 RPM	23.51 RPM
SRP007412_heart	0.06 RPM	8.36 RPM
SRP007412_kidney	0.00 RPM	19.48 RPM
SRP007412_liver	0.00 RPM	5.98 RPM
SRP007412_testis	0.15 RPM	21.60 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2135 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2135 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2135 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010432	2 retrocopies	retro_chof_1794, retro_chof_234,
Dasypus novemcinctus	ENSDNOG00000011053	2 retrocopies	retro_dnov_1377, retro_dnov_542,
Homo sapiens	ENSG00000163512	2 retrocopies	retro_hsap_1491, retro_hsap_1564,
Gorilla gorilla	ENSGGOG00000022881	2 retrocopies	retro_ggor_1145, retro_ggor_1189,
Loxodonta africana	ENSLAFG00000008538	2 retrocopies	retro_lafr_529, retro_lafr_925,
Myotis lucifugus	ENSMLUG00000000043	3 retrocopies	retro_mluc_1707, retro_mluc_435, retro_mluc_611,
Macaca mulatta	ENSMMUG00000000056	1 retrocopy	retro_mmul_2135 ,
Monodelphis domestica	ENSMODG00000015075	1 retrocopy	retro_mdom_1786,
Nomascus leucogenys	ENSNLEG00000004069	1 retrocopy	retro_nleu_1714,
Oryctolagus cuniculus	ENSOCUG00000014956	1 retrocopy	retro_ocun_1778,
Otolemur garnettii	ENSOGAG00000005896	1 retrocopy	retro_ogar_3078,
Pongo abelii	ENSPPYG00000014053	2 retrocopies	retro_pabe_1241, retro_pabe_3784,
Pan troglodytes	ENSPTRG00000014707	1 retrocopy	retro_ptro_1052,
Tursiops truncatus	ENSTTRG00000016434	1 retrocopy	retro_ttru_1093,