RetrogeneDB ID: retro_mdom_1778

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:63937058..63937823(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000001763
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BECN1
• Ensembl ID: ENSMODG00000015064
• Aliases: None
• Description: beclin 1, autophagy related [Source:HGNC Symbol;Acc:1034]

Sequence

>retro_mdom_1778
CTAGAGGTCACTGGAGATCTTTTTGATATCATGTCAGGTCAGACAGATGTGGCTCACCCTTTGTGTGAGGAATGTACAGA
TACTTTGTTGGATCAGCTGGACACCCAGCTCAACATCACAGAAAATGAATGTCAGAACTACAAATGCTGTTTGGAGATCT
TGGAGCAAATGAATGAAGATGAGGAGGAGAAGTTGAAGATGGAATTACAGGAGCTGGCACTTGAGGAAGAAAGGCTGATC
CAGGAACTGGAAGGTGTAGAAAAGAACCACAAAATTGTGGCAGAAGATCTTGAGAAAGTCCAGGCAGAGACTGAGCAGCT
AGATCAGGAGGAAGCTCAATACCAGAGGGAATATAGTGAGTTTAAACAAGAGTTGGAGCTAGATGATGAGCTAAAGAGTA
TGGACAACCCATATGCCCAGATCCAACTAGACAAGCTGAAGAAAACAAATGTTTTTAATGCAACATTCCACATCTGGCAT
AGGGGACAGTGTGGTACAATTAATAACTTTAGGCTGGGGCAGCTTCCTAGTGTCCCTGTGGAATGGAATGAGATCAACGC
TGCGTGGGGGCAGACAGTATTGCTGCTCCATGCCCTGGCCAATAAAATGGGCCTGAAATTTCAGAGGTATAGCCTTGTTC
CTTATGGAAATCATTCCTATTTGGTGTCTCTCACAGACAAATCCAAGGAGCTGCCATTATACTGTTCTGGGGGCTTGCAG
TTTTTCTGGGACAACAAGTTTGACCATGCAATGGTGACTGGATTG

Alignment

ORF - retro_mdom_1778 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.47 %
• Parental protein coverage: 57.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNITENECQNYKRCLEILEQMNEDDEEKLKMELK
          L.VTGDLFDIMSGQTDV.HPLCEECTDTLLDQLDTQLNITENECQNYK.CLEILEQMNED.EEKLKMEL.
Retrocopy LEVTGDLFDIMSGQTDVAHPLCEECTDTLLDQLDTQLNITENECQNYKCCLEILEQMNEDEEEKLKMELQ

Parental  ELALEEERLIQELEDVEKNRKIVAEDLEKVQAETERLDQEEAQYQREYSEFKRQQLELDDELKSVDNQMR
          ELALEEERLIQELE.VEKN.KIVAEDLEKVQAETE.LDQEEAQYQREYSEFK.Q.LELDDELKS.DN...
Retrocopy ELALEEERLIQELEGVEKNHKIVAEDLEKVQAETEQLDQEEAQYQREYSEFK-QELELDDELKSMDNP--

Parental  YAQIQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANKMGLKF
          YAQIQLDKLKKTNVFNATFHIWH.GQ.GTINNFRLG.LPSVPVEWNEINAAWGQTVLLLHALANKMGLKF
Retrocopy YAQIQLDKLKKTNVFNATFHIWHRGQCGTINNFRLGQLPSVPVEWNEINAAWGQTVLLLHALANKMGLKF

Parental  QRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFL
          QRY.LVPYGNHSYL.SLTDKSKELPLYCSGGL.FFWDNKFDHAMV..L
Retrocopy QRYSLVPYGNHSYLVSLTDKSKELPLYCSGGLQFFWDNKFDHAMVTGL

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_1778 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1778 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 18 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006867	1 retrocopy	retro_amel_16,
Bos taurus	ENSBTAG00000019914	1 retrocopy	retro_btau_226,
Callithrix jacchus	ENSCJAG00000013144	1 retrocopy	retro_cjac_330,
Dipodomys ordii	ENSDORG00000000956	1 retrocopy	retro_dord_675,
Felis catus	ENSFCAG00000013136	1 retrocopy	retro_fcat_62,
Homo sapiens	ENSG00000126581	1 retrocopy	retro_hsap_335,
Macropus eugenii	ENSMEUG00000011700	1 retrocopy	retro_meug_600,
Macaca mulatta	ENSMMUG00000029971	1 retrocopy	retro_mmul_81,
Monodelphis domestica	ENSMODG00000015064	1 retrocopy	retro_mdom_1778 ,
Mus musculus	ENSMUSG00000035086	1 retrocopy	retro_mmus_390,
Nomascus leucogenys	ENSNLEG00000011840	1 retrocopy	retro_nleu_1776,
Oryctolagus cuniculus	ENSOCUG00000015964	3 retrocopies	retro_ocun_1021, retro_ocun_1732, retro_ocun_218,
Procavia capensis	ENSPCAG00000014049	1 retrocopy	retro_pcap_345,
Pan troglodytes	ENSPTRG00000022819	1 retrocopy	retro_ptro_268,
Sorex araneus	ENSSARG00000000367	1 retrocopy	retro_sara_136,
Sus scrofa	ENSSSCG00000017386	1 retrocopy	retro_sscr_75,
Ictidomys tridecemlineatus	ENSSTOG00000012612	1 retrocopy	retro_itri_25,
Tursiops truncatus	ENSTTRG00000011716	1 retrocopy	retro_ttru_595,