RetrogeneDB ID: retro_mdom_2006

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:69811261..69812083(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000005348
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP6V1C2
• Ensembl ID: ENSMODG00000014803
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2 [Source:HGNC Symbol;Acc:18264]

Sequence

>retro_mdom_2006
TCAGAGTTTTGGTTAATTTCTATTCCTGGAGATGAGGAAAATTTGAGGATCCTGGAGCGGATGAAGAATCTTACCTCCAA
GGCCAACCTGTGCCGCAATTCCAACTTTGCTATTCCTGATTTCAAGGTGGGGACCTTAGATTCTCTCATTAGCCTCTCAG
ATGAGTTGGGGAAACTTGATCATTTGGCCGAAAGTCTCGTGAAGAGAATGGTTCAGTGTGTTATAGAACAGAAGAAATTC
AAGAACGGTGAATTTCAGGAGTACCTTTTGGTCACTGGAGTTTCCTTAGCTTCTTTTGTGACTCACTTTGAATGGGATAT
GGCCAGGTATTCTGCCCAGCAACCATTGTGGACTATAGTGGATAAGTTAGGGAAGCAGCTGACCCAAATGGAGACTGATC
TAAAAACCAGAATCTCAGTCTACAACAAACAGAAAAGACATCTGGAGAATATGGAAGAGAAATTGACAGGCAACCTCTTT
AGCAGGTCACTATCAGATATTGTGAGCAAAGAGGATTTTGTGTTGGATTCAGAATATCTCATCACCCTCCTGGTAATTGT
TCCAAAAGCAAGCTATTCTAAGTGGCAGAAAACTTACGAATCCCTCTCTGACATGGTGGTCCCTCGGTCAACCAAACTGA
TTGCTGAAGACAAAGAGGATGGCCTCTTCACCGTCACCATGTTCCGTCAAGTGATTAATGAGTTCAAAGCCAAAGCTGCA
GCCAACAAGTTCACTGTTCGAGACTTTTTCTATGATGAAAAAGAAATTCAAAGAGAACGGGAATTGCTAAACAAGTTGCT
TTCAGCGAAGAAACAACAATAT

Alignment

ORF - retro_mdom_2006 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.98 %
• Parental protein coverage: 71.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEFWLISAPGDKENLQALERMNTVTSKSNLSHNTKFAIPDFKVGTLDSLVGLSDELGKLDSFAESLIKKM
          SEFWLIS.PGD.ENL..LERM...TSK.NL..N..FAIPDFKVGTLDSL..LSDELGKLD..AESL.K.M
Retrocopy SEFWLISIPGDEENLRILERMKNLTSKANLCRNSNFAIPDFKVGTLDSLISLSDELGKLDHLAESLVKRM

Parental  AQCVVEVMEDAKGRVHENLLANGVDLTSFVTRFEWDMAKYPAKQPLVVVVDTLEKQLAQIETDLKTRTAA
          .QCV.E......G...E.LL..GV.L.SFVT.FEWDMA.Y.A.QPL...VD.L.KQL.Q.ETDLKTR...
Retrocopy VQCVIEQKKFKNGEFQEYLLVTGVSLASFVTHFEWDMARYSAQQPLWTIVDKLGKQLTQMETDLKTRISV

Parental  YNTLKGNLENLERKSSGNLLTRTLADIVNKEDFVLDSEYLVTLVVIVQKPNYSQWQKTYESLSDMVVPRS
          YN..K..LEN.E.K..GNL..R.L.DIV.KEDFVLDSEYL.TL.VIV.K..YS.WQKTYESLSDMVVPRS
Retrocopy YNKQKRHLENMEEKLTGNLFSRSLSDIVSKEDFVLDSEYLITLLVIVPKASYSKWQKTYESLSDMVVPRS

Parental  TKLIAEDNEGGLFTVTLFRRVIDDFKVKAREKKFIVREFFYDEKEIKTEREEMTKLLSEKKQQY
          TKLIAED.E.GLFTVT.FR.VI..FK.KA...KF.VR.FFYDEKEI..ERE...KLLS.KKQQY
Retrocopy TKLIAEDKEDGLFTVTMFRQVINEFKAKAAANKFTVRDFFYDEKEIQRERELLNKLLSAKKQQY

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	1.79 RPM
SRP007412_cerebellum	0.00 RPM	0.65 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	130.37 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.20 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_2006 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2006 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001927	1 retrocopy	retro_btau_1823,
Callithrix jacchus	ENSCJAG00000006660	2 retrocopies	retro_cjac_1089, retro_cjac_3461,
Monodelphis domestica	ENSMODG00000014803	1 retrocopy	retro_mdom_2006 ,
Otolemur garnettii	ENSOGAG00000009748	1 retrocopy	retro_ogar_403,
Sarcophilus harrisii	ENSSHAG00000009886	1 retrocopy	retro_shar_33,