RetrogeneDB ID: retro_mdom_1664

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:92940428..92941124(-)
• Located in intron of: ENSMODG00000002554

Retrocopy information

• Ensembl ID: ENSMODG00000002424
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: YWHAZ
• Ensembl ID: ENSMODG00000006158
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide [Source:HGNC Symbol;Acc:12855]

Sequence

>retro_mdom_1664
ATGGAAAAAAATGAGCTGGTGCCAAAGGGCAAATTGGCTGAGCAGGCTGAGAGATATGATGACATGGCATCCTGCATGAA
GTCTGTAACTGAGCAAGGAGCTGAATTATCCAATGAGGAGAGGAATCTTCTCTTTGTTGCTTACAAAAATGTCATAGATG
CCCAAAGGTCATCTTGGAGGGTCATTTAAAGTATTGAACAAAAGACAGAAGGTGCTGAGAAAAAAACAGCAGATGGCCCA
AGAATAGAGAGAAAATCGAGATGGAACTAAGAGATATCTGCAATGATGTGCTGTCTCTATTGGAAAAGTTCTTGATTCCT
AATGTTTTATAAGCAAAAAGACAGTTTTCTCATTGAAAATGAAAGGAGACTAAAAACAGTTTCTTGGCTGAGGTTGCTGA
TGGTGATGACAAGAAAGGTATAAGTGGATCAATCATGACAAGCATATCAAGAAGCATTTGAAATTAGCAAAAAGGAGTTG
CAACCAACACAGTCTATAAGATTGGGTCTGGCCTTGAATTTTTCTGTGTTCTTTTATGAGATCCTGAACTCTCCAGAGAG
TCTGCTCCCTTGCAAAGATAGCTTTTGATGAAGCCAGTGTCAAACTTAATACATTAAGTGAGAATCATACAAAGACAGCA
CACTAACAATGCAATTACCAAGAGACAACTTGACATAGTGGACATTGGACACGCAG

Alignment

ORF - retro_mdom_1664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.15 %
• Parental protein coverage: 95.1 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTE
          M.KNELV.K.KLAEQAERYDDMA.CMKSVTEQGAELSNEERNLL.VAYKNV..A.RSSWRV..SIEQKTE
Retrocopy MEKNELVPKGKLAEQAERYDDMASCMKSVTEQGAELSNEERNLLFVAYKNVIDAQRSSWRVI*SIEQKTE

Parental  GAEK-KQQMAREYREKIETELRDICNDVLSLLEKFLIPNASQAESK-VFYLKMKGDYYRYL-AEVAAGDD
          GAEK.K.......REKIE.ELRDICNDVLSLLEKFLIPN...A....VF.LKMKGD....L.AEVA.GDD
Retrocopy GAEK<KNSRWPKNREKIEMELRDICNDVLSLLEKFLIPNVL*AKRQ<VFSLKMKGD*KQFL>AEVADGDD

Parental  KKGI-VDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAF-DEAIAELDT
          KKGI.VDQS.QAYQEAFEISKKE.QPT..IRLGLALNFSVF.YEILNSPE......K..F.DEA...L.T
Retrocopy KKGI>VDQS*QAYQEAFEISKKELQPTQSIRLGLALNFSVFFYEILNSPESLLP-CKDSF>DEASVKLNT

Parental  LSE-ESYKDSTLIMQLLRDNLTLWTSDTQ
          LSE.ESYKDSTL.MQL.RDNLT.WT.DTQ
Retrocopy LSE<ESYKDSTLTMQLPRDNLT*WTLDTQ

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1664 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1664 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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 72 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,
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,
Monodelphis domestica	ENSMODG00000006158	8 retrocopies	retro_mdom_1589, retro_mdom_1664 , retro_mdom_1763, retro_mdom_1815, retro_mdom_1875, retro_mdom_1958, retro_mdom_255, retro_mdom_446,
Monodelphis domestica	ENSMODG00000010174	2 retrocopies	retro_mdom_1567, retro_mdom_744,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Monodelphis domestica	ENSMODG00000016200	2 retrocopies	retro_mdom_1557, retro_mdom_212,
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,
Ochotona princeps	ENSOPRG00000000276	3 retrocopies	retro_opri_1218, retro_opri_218, retro_opri_967,
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,