RetrogeneDB ID: retro_mdom_1656

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:61038171..61038645(-)
• Located in intron of: ENSMODG00000007622

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010003
• Aliases: None
• Description: None

Sequence

>retro_mdom_1656
ATTCAGAAGTTCAAGCTTTGGGATAATGAGATGCAATATGTAGACCAACTTCTCAAAAAGGATGTGAGAAATAACTCTGT
GTGGAACCAAAGACACTTAGTAATTTCTAACACTTCAGGCTACAAAGGTCCTGCTATCCTGGAGAGATAAGTTCAATATA
CTCTAGAAATTATAAAAACTGCACCACATAATGAAAGTGCATGGAATTATTTTAAAAGGATTCTGCAAGATCATGATCTT
TCCAAGTATCCCATCCTTTTAGAGCAGTTGTTAGATTTACAGCCAAGTCACAGTTCTCCCTATCTGATCATCTTTCTTGT
GGATATATATGAAGATATGTTAGAAAACCAATGTGACAACAAGGAAGACATGCTTAATAAAGCATTAGAGTTATGTGAAA
TGCTAGCTAAAGAAAAAGACACTTCTATAAGAAAGGAATATTGGTGATATAGTGGAAGATCCCTTCAAAACAAA

Alignment

ORF - retro_mdom_1656 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.44 %
• Parental protein coverage: 52.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IHEYPLWDLELQYVDQLLKVDVRNNSVWNQRHFVISNTSGYNDPAILEREVQYTLEMIKTAPHNESAWNY
          I....LWD.E.QYVDQLLK.DVRNNSVWNQRH.VISNTSGY..PAILER.VQYTLE.IKTAPHNESAWNY
Retrocopy IQKFKLWDNEMQYVDQLLKKDVRNNSVWNQRHLVISNTSGYKGPAILER*VQYTLEIIKTAPHNESAWNY

Parental  LKGILQDRGLSKYPNLLEQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKEDTLNKALELCEILAKEKD
          .K.ILQD..LSKYP.LLEQLLDLQPSHSSPYLI.FLVDIYEDMLENQCDNKED.LNKALELCE.LAKEKD
Retrocopy FKRILQDHDLSKYPILLEQLLDLQPSHSSPYLIIFLVDIYEDMLENQCDNKEDMLNKALELCEMLAKEKD

Parental  T-IRKEYWRYIGRSLQNK
          T.IRKEYW.Y.GRSLQNK
Retrocopy TSIRKEYW*YSGRSLQNK

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	56.14 RPM
SRP007412_cerebellum	0.00 RPM	62.35 RPM
SRP007412_heart	0.00 RPM	50.83 RPM
SRP007412_kidney	0.00 RPM	75.06 RPM
SRP007412_liver	0.00 RPM	71.50 RPM
SRP007412_testis	0.00 RPM	75.63 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1656 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1656 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003201	2 retrocopies	retro_btau_1431, retro_btau_1768,
Canis familiaris	ENSCAFG00000005385	1 retrocopy	retro_cfam_941,
Erinaceus europaeus	ENSEEUG00000008272	1 retrocopy	retro_eeur_532,
Homo sapiens	ENSG00000168522	1 retrocopy	retro_hsap_805,
Loxodonta africana	ENSLAFG00000000631	1 retrocopy	retro_lafr_506,
Macaca mulatta	ENSMMUG00000017158	1 retrocopy	retro_mmul_1078,
Monodelphis domestica	ENSMODG00000010003	1 retrocopy	retro_mdom_1656 ,
Nomascus leucogenys	ENSNLEG00000012979	1 retrocopy	retro_nleu_2408,
Pteropus vampyrus	ENSPVAG00000013502	2 retrocopies	retro_pvam_1157, retro_pvam_1433,
Sorex araneus	ENSSARG00000009660	1 retrocopy	retro_sara_109,
Ictidomys tridecemlineatus	ENSSTOG00000011626	1 retrocopy	retro_itri_1221,
Tursiops truncatus	ENSTTRG00000008870	1 retrocopy	retro_ttru_579,