RetrogeneDB ID: retro_mmul_2422

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:105377498..105378229(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2328
• Ensembl ID: ENSMMUG00000006489
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide [Source:RefSeq peptide;Acc:NP_001247828]

Sequence

>retro_mmul_2422
ATGGATAAAAATGAGCTGGTTCAGAAGACCAAACTGGCTGAGCAGGCTGAGCGATATGATAGCATGGCAGCCTGCATGAA
GTCTGTATCTGAGCAAGGAGCTGAATTATCCAATGAGGAGAAAAATCTTCTCTCAGTTGCTTATAAAAATGTTGTAGGAG
CCCGTAGGCCATCTTAGATGGTCATCTCAAGTATTGAACAAAAGACGGAAGATGCTAAGGAAAAACAGCAGATGGCTCGA
AAATACAGAGAGAAAATTGAGATGGAGCTAAGAGATATCTACAATGATGTACTGTCTCTTTTGGAAAAGTTCTTGATCCC
CAGCGCTTCACAAGCAGAGAGCAAAGTTTTCTATTTGAAAATGAAAGGAGATTACTACCATTACTTGGCTGAGGTTGCCA
CTGGTGATGACAAGAAAGGGATTGTGGATCAGTCACAACAAGCATACCAAGAAGCTTTTGAAATCAGTGAAAAGGAAATG
CAGCCGACACATCCTATCAGACTGGGTCGGGCCCTTAACTTCTCTTGTTCTATTATGAGATTCTGAACTCCCCAGATAAA
GCCTGCTCCCTTGCAAAGATGGCTTTTGATGAAGCCATTGCTGAACCTGATACATTAAGTGAAGAGTCATACAAAGACAG
CACACTAATAATGCAATTACCGAGAGACGACTTGACATTGTGGACATTGGATACCTAAGGAGACAAAGCTGAAGCAGGAG
AAATGGGAAAA

Alignment

ORF - retro_mmul_2422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.35 %
• Parental protein coverage: 99.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTE
          MDKNELVQK.KLAEQAERYD.MAACMKSV.EQGAELSNEE.NLLSVAYKNVVGARR.S..V.SSIEQKTE
Retrocopy MDKNELVQKTKLAEQAERYDSMAACMKSVSEQGAELSNEEKNLLSVAYKNVVGARRPS*MVISSIEQKTE

Parental  GAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKG
          .A..KQQMAR.YREKIE.ELRDI.NDVLSLLEKFLIP.ASQAESKVFYLKMKGDYY.YLAEVA.GDDKKG
Retrocopy DAKEKQQMARKYREKIEMELRDIYNDVLSLLEKFLIPSASQAESKVFYLKMKGDYYHYLAEVATGDDKKG

Parental  IVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFS-VFYYEILNSPEKACSLAKTAFDEAIAELDTLSEE
          IVDQSQQAYQEAFEIS.KEMQPTHPIRLG.ALNFS..FYYEILNSP.KACSLAK.AFDEAIAE.DTLSEE
Retrocopy IVDQSQQAYQEAFEISEKEMQPTHPIRLGRALNFS<LFYYEILNSPDKACSLAKMAFDEAIAEPDTLSEE

Parental  SYKDSTLIMQLLRDNLTLWTSDTQGDEAEAGEGGE
          SYKDSTLIMQL.RD.LTLWT.DT.GD.AEAGE.G.
Retrocopy SYKDSTLIMQLPRDDLTLWTLDT*GDKAEAGEMGK

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	470.05 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	603.38 RPM
SRP007412_cerebellum	0.00 RPM	291.68 RPM
SRP007412_heart	0.00 RPM	88.86 RPM
SRP007412_kidney	0.00 RPM	112.56 RPM
SRP007412_liver	0.00 RPM	31.79 RPM
SRP007412_testis	0.04 RPM	133.55 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2422 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2422 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2422 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_556

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 97 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008694	2 retrocopies	retro_acar_25, retro_acar_44,
Bos taurus	ENSBTAG00000000236	4 retrocopies	retro_btau_1482, retro_btau_635, retro_btau_68, retro_btau_910,
Canis familiaris	ENSCAFG00000000580	6 retrocopies	retro_cfam_1302, retro_cfam_1521, retro_cfam_158, retro_cfam_1840, retro_cfam_233, retro_cfam_465,
Choloepus hoffmanni	ENSCHOG00000002798	9 retrocopies	retro_chof_1572, retro_chof_1703, retro_chof_1890, retro_chof_2321, retro_chof_2346, retro_chof_2669, retro_chof_292, retro_chof_315, retro_chof_933,
Callithrix jacchus	ENSCJAG00000015844	5 retrocopies	retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
Cavia porcellus	ENSCPOG00000020285	5 retrocopies	retro_cpor_220, retro_cpor_323, retro_cpor_434, retro_cpor_592, retro_cpor_644,
Dasypus novemcinctus	ENSDNOG00000001672	10 retrocopies	retro_dnov_1007, retro_dnov_117, retro_dnov_1354, retro_dnov_1579, retro_dnov_1769, retro_dnov_1907, retro_dnov_1993, retro_dnov_2588, retro_dnov_892, retro_dnov_99,
Ficedula albicollis	ENSFALG00000005860	1 retrocopy	retro_falb_13,
Felis catus	ENSFCAG00000032017	4 retrocopies	retro_fcat_1563, retro_fcat_1631, retro_fcat_1697, retro_fcat_60,
Gallus gallus	ENSGALG00000010725	1 retrocopy	retro_ggal_3,
Gorilla gorilla	ENSGGOG00000022133	9 retrocopies	retro_ggor_1092, retro_ggor_1754, retro_ggor_211, retro_ggor_2379, retro_ggor_2997, retro_ggor_2998, retro_ggor_3020, retro_ggor_499, retro_ggor_544,
Loxodonta africana	ENSLAFG00000004944	2 retrocopies	retro_lafr_1089, retro_lafr_112,
Myotis lucifugus	ENSMLUG00000017323	3 retrocopies	retro_mluc_1617, retro_mluc_1686, retro_mluc_296,
Macaca mulatta	ENSMMUG00000006489	7 retrocopies	retro_mmul_1859, retro_mmul_1883, retro_mmul_2136, retro_mmul_2247, retro_mmul_2422 , retro_mmul_2503, retro_mmul_451,
Macaca mulatta	ENSMMUG00000013206	3 retrocopies	retro_mmul_1061, retro_mmul_236, retro_mmul_673,
Mus musculus	ENSMUSG00000022285	3 retrocopies	retro_mmus_163, retro_mmus_2187, retro_mmus_744,
Oryctolagus cuniculus	ENSOCUG00000000734	2 retrocopies	retro_ocun_1091, retro_ocun_248,
Pongo abelii	ENSPPYG00000018791	7 retrocopies	retro_pabe_103, retro_pabe_1242, retro_pabe_2047, retro_pabe_3417, retro_pabe_3740, retro_pabe_556, retro_pabe_89,
Pelodiscus sinensis	ENSPSIG00000003703	1 retrocopy	retro_psin_13,
Sarcophilus harrisii	ENSSHAG00000012671	2 retrocopies	retro_shar_126, retro_shar_409,
Sus scrofa	ENSSSCG00000006062	2 retrocopies	retro_sscr_222, retro_sscr_35,
Ictidomys tridecemlineatus	ENSSTOG00000023864	3 retrocopies	retro_itri_162, retro_itri_483, retro_itri_887,
Taeniopygia guttata	ENSTGUG00000012078	1 retrocopy	retro_tgut_4,
Tursiops truncatus	ENSTTRG00000015906	4 retrocopies	retro_ttru_15, retro_ttru_1540, retro_ttru_207, retro_ttru_455,
Vicugna pacos	ENSVPAG00000005865	1 retrocopy	retro_vpac_350,