RetrogeneDB ID: retro_mdom_1567

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:302129888..302130305(-)
• Located in intron of: ENSMODG00000007240

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSMODG00000010174
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide [Source:HGNC Symbol;Acc:12851]

Sequence

>retro_mdom_1567
AAAGGCAAGGTTTTCTATTATAAAATGAAAGTAGCCTGTCTCAGGTATCTGGCTGAATTTGTCACAGGAAATGACTTAAA
GTAGGCTATAGAGAATACGCTGGTGGTTTATAAAGCTTCTAGTGATATTGTAGTGACAGAACTTCCACCAGTGCACTCCA
TCTGCTTAGGTCTTGCTCACAACTTTTCTGTATTCTACTAGGAAATTATTAATTTCCCTGACCATGCCTGCAGGTTGGCA
AAAGCAGCCTTCAATGATGCAATTGCAGAACTCGATACACTGATTGAAGAAAGCGATGAGGACGTGACACTTATAATGCA
GTTGTTACATGATAACCTGACTCTGTGGACTTCAGATATGCAGGGTGATGGTGAAGAACAGAATAAAGAAGTGCTGCAGG
ATATGGAAGATGAAAAC

Alignment

ORF - retro_mdom_1567 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.7 %
• Parental protein coverage: 53.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEIL
          ..KVFYYKMK....RYLAEF.TGND.K.A.EN.LV.YKA.SDI..TELPP.H.I.LGLA.NFSVFY.EI.
Retrocopy KGKVFYYKMKVACLRYLAEFVTGNDLK*AIENTLVVYKASSDIVVTELPPVHSICLGLAHNFSVFY*EII

Parental  NSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDGEEQNKEALQDVEDEN
          N.PD.ACRLAKAAF.DAIAELDTL.EES..D.TLIMQLL.DNLTLWTSDMQGDGEEQNKE.LQD.EDEN
Retrocopy NFPDHACRLAKAAFNDAIAELDTLIEESDEDVTLIMQLLHDNLTLWTSDMQGDGEEQNKEVLQDMEDEN

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_1567 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1567 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 17 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005664	3 retrocopies	retro_btau_1485, retro_btau_372, retro_btau_954,
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912, retro_chof_905,
Ciona intestinalis	ENSCING00000023856	1 retrocopy	retro_cint_15,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9,
Echinops telfairi	ENSETEG00000012056	2 retrocopies	retro_etel_1762, retro_etel_738,
Homo sapiens	ENSG00000108953	4 retrocopies	retro_hsap_2324, retro_hsap_3739, retro_hsap_3851, retro_hsap_4703,
Gorilla gorilla	ENSGGOG00000016840	1 retrocopy	retro_ggor_2596,
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,
Nomascus leucogenys	ENSNLEG00000000656	2 retrocopies	retro_nleu_2067, retro_nleu_2868,
Otolemur garnettii	ENSOGAG00000006155	2 retrocopies	retro_ogar_1003, retro_ogar_2144,
Pongo abelii	ENSPPYG00000007769	4 retrocopies	retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,
Pan troglodytes	ENSPTRG00000008521	5 retrocopies	retro_ptro_1697, retro_ptro_2538, retro_ptro_2624, retro_ptro_2626, retro_ptro_2993,
Ictidomys tridecemlineatus	ENSSTOG00000005084	1 retrocopy	retro_itri_1175,
Vicugna pacos	ENSVPAG00000010288	3 retrocopies	retro_vpac_230, retro_vpac_411, retro_vpac_559,