RetrogeneDB ID: retro_amel_562

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192502.1:668872..669519(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAZ
• Ensembl ID: ENSAMEG00000000328
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide [Source:HGNC Symbol;Acc:12855]

Sequence

>retro_amel_562
ATGGGTAGAAACGAGCTGGTGCAGAAGGTCAAACTGGCTGAGCAGGCTGAGTGTTAAGATTACATGGCAGCCTGCATGAA
GTCTGTAACTGAGCAAAAAGCTGAATTATTCAATGAGGAGAGGAATCTTCTCTCATTTGCTTATAAAAATGTTGTAGGAG
CCCATAGGTCATCTTGGAGGCTTGTCTCAGGAATTTAGCAAAAGATGGAAGGTGATGAGAAAAAACAGCAGACGGCTTGA
GAATACAGAGAGAAAATTGAGACCAAGCCAAAAGATTTCTGCAATGATGTATGGTCTCTTTTGGGAAGTTTTTGATCCCC
AGTGCTTCACAGGTGAGCAAAGTCTTCTATTTGAAAATGAATGGAGATGACTACTGTTACTTGGCCGGGGTTTCTGCTGG
TGACGATAAGAAGGACATTATGGATCAGTCACCACAGCGATACCAAGAAACTCCTGAAATCAGCAAAAAGGAAATGCAAC
CAATACATCCTATCAGGTTGGGTCTGGCCCTTAACTTCTCTGTGTTCTATTGTAAGATTCTGAACTCCCTGAAGAAAGCC
TGCTCTCTTGCAAAGACACCTTTTGATAAAGCCATTGCTGAACTTGATACATTAAGTGAAGAGTCATACCAAGACAGCCC
TTTTGTA

Alignment

ORF - retro_amel_562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.52 %
• Parental protein coverage: 88.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTE
          M..NELVQK.KLAEQAE..D.MAACMKSVTEQ.AEL.NEERNLLS.AYKNVVGA.RSSWR.VS.I.QK.E
Retrocopy MGRNELVQKVKLAEQAEC*DYMAACMKSVTEQKAELFNEERNLLSFAYKNVVGAHRSSWRLVSGI*QKME

Parental  GAEKKQQMAREYREKIETELRDICNDVLSLLE-KFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKK
          G.EKKQQ.A.EYREKIET...D.CNDV.SLL..KFLIP.ASQ..SKVFYLKM.GD.Y.YLA.V.AGDDKK
Retrocopy GDEKKQQTA*EYREKIETKPKDFCNDVWSLLG<KFLIPSASQV-SKVFYLKMNGDDYCYLAGVSAGDDKK

Parental  GIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEE
          .I.DQS.Q.YQE..EISKKEMQP.HPIRLGLALNFSVFY..ILNS..KACSLAKT.FD.AIAELDTLSEE
Retrocopy DIMDQSPQRYQETPEISKKEMQPIHPIRLGLALNFSVFYCKILNSLKKACSLAKTPFDKAIAELDTLSEE

Parental  SYKDSTLI
          SY.DS...
Retrocopy SYQDSPFV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_562 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_562 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008694	2 retrocopies	retro_acar_25, retro_acar_44,
Ailuropoda melanoleuca	ENSAMEG00000000328	1 retrocopy	retro_amel_562 ,
Ailuropoda melanoleuca	ENSAMEG00000008618	4 retrocopies	retro_amel_1214, retro_amel_1382, retro_amel_1837, retro_amel_917,
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,
Callithrix jacchus	ENSCJAG00000015844	5 retrocopies	retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
Equus caballus	ENSECAG00000021882	3 retrocopies	retro_ecab_202, retro_ecab_31, retro_ecab_624,
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,
Homo sapiens	ENSG00000164924	1 retrocopy	retro_hsap_549,
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,
Mustela putorius furo	ENSMPUG00000015158	4 retrocopies	retro_mputfur_1000, retro_mputfur_239, retro_mputfur_7, retro_mputfur_864,
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,
Pteropus vampyrus	ENSPVAG00000016641	1 retrocopy	retro_pvam_1101,
Sarcophilus harrisii	ENSSHAG00000012671	2 retrocopies	retro_shar_126, retro_shar_409,
Sus scrofa	ENSSSCG00000006062	2 retrocopies	retro_sscr_222, retro_sscr_35,
Taeniopygia guttata	ENSTGUG00000012078	1 retrocopy	retro_tgut_4,
Tarsius syrichta	ENSTSYG00000006150	10 retrocopies	retro_tsyr_1047, retro_tsyr_1075, retro_tsyr_1419, retro_tsyr_1941, retro_tsyr_2022, retro_tsyr_2066, retro_tsyr_2085, retro_tsyr_720, retro_tsyr_900, retro_tsyr_985,