RetrogeneDB ID: retro_nleu_487

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397266.1:19097488..19098057(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAZ
• Ensembl ID: ENSNLEG00000003220
• Aliases: None
• Description: None

Sequence

>retro_nleu_487
ATGGATAAAAATGAGCTGGTTGAGAAGGCCAAACTGGCCCAGTAGGCTGAGAGATATGATGACATGGCAGCCTGCATGAA
ATCTGTTAACTGAGCAAGGAGCTGAAATTGTCCAATGAGGAGAGGAACCTTCTCTCAGTTGCTTCTAAAAATGTTGTAGG
AGCCTATAGGTCATCTTAGAGGGTTGTCTCAAGTATTGAACAAAAGACAGAAGGTGCTGAGAGAAAACAGCAGGTGGCTC
GAGAATACAGAGAGAAAATTCAGACACAGCTAAGAGATATCTGCAATGATGTACTGTCTCTTTTGGAAAAGTTCTTGATC
CCCAGTGCTTCACAAGCAGAGAGCAAAGTCTTTTATTTGAAAATGAAAGGAGATTACTACCGTTACTTGGCTGAGGTTGT
TGCTGGTGATGACAAGAAAGGGATTGTGGATCAGTCACAACAAGCATACCAAGAAGCTTTTGAAATCAGCAAAAAGGAAA
TGCAACCAACACATCCTATCAGACTGGGTCTGGCCCTTTACTCCTCTGTGTTCTATTACGAGATTCTGAACTCCCCAGGG
AAAGCCTGC

Alignment

ORF - retro_nleu_487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.1 %
• Parental protein coverage: 77.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDKNELVQKAKLAEQAERYDDMAACMKSV-TEQGAE-LSNEERNLLSVAYKNVVGARRSSWRVVSSIEQK
          MDKNELV.KAKLA..AERYDDMAACMKSV.TEQGAE.LSNEERNLLSVA.KNVVGA.RSS.RVVSSIEQK
Retrocopy MDKNELVEKAKLAQ*AERYDDMAACMKSV>TEQGAE>LSNEERNLLSVASKNVVGAYRSS*RVVSSIEQK

Parental  TEGAEKKQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDK
          TEGAE.KQQ.AREYREKI.T.LRDICNDVLSLLEKFLIP.ASQAESKVFYLKMKGDYYRYLAEV.AGDDK
Retrocopy TEGAERKQQVAREYREKIQTQLRDICNDVLSLLEKFLIPSASQAESKVFYLKMKGDYYRYLAEVVAGDDK

Parental  KGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKAC
          KGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLAL..SVFYYEILNSP.KAC
Retrocopy KGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALYSSVFYYEILNSPGKAC

Legend:

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

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_487 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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 20 parental genes, and 74 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,
Callithrix jacchus	ENSCJAG00000015844	5 retrocopies	retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
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,
Mus musculus	ENSMUSG00000022285	3 retrocopies	retro_mmus_163, retro_mmus_2187, retro_mmus_744,
Nomascus leucogenys	ENSNLEG00000000656	2 retrocopies	retro_nleu_2067, retro_nleu_2868,
Nomascus leucogenys	ENSNLEG00000003220	7 retrocopies	retro_nleu_1368, retro_nleu_1426, retro_nleu_2186, retro_nleu_23, retro_nleu_449, retro_nleu_487 , retro_nleu_722,
Nomascus leucogenys	ENSNLEG00000006643	2 retrocopies	retro_nleu_42, retro_nleu_422,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
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,
Taeniopygia guttata	ENSTGUG00000012078	1 retrocopy	retro_tgut_4,