RetrogeneDB ID: retro_mdom_1509

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:61107181..61108589(-)
• Located in intron of: ENSMODG00000020807

Retrocopy information

• Ensembl ID: ENSMODG00000025124
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBA2
• Ensembl ID: ENSMODG00000011934
• Aliases: None
• Description: ubiquitin-like modifier activating enzyme 2 [Source:HGNC Symbol;Acc:30661]

Sequence

>retro_mdom_1509
CAGAAAACTTTCCTGGGATGTACAATTCGTAACACCCCTTCAGAACCTATCCACTGTATTGTATGGGCAAAATATTTGTT
CAACTAGTTGTTTGGGGAAGAAGATGCTGATCAGGAAGTATCCCCTGACAGAGCTGATCCTGAAACTGCTTGGGAACCAG
CAGAAGCTGAAGCCAGAGCAAGAGCGTCTAATGATGATGGTGATATTAAGTGTATTTCCACTAAAGAATGGGCTAAATCA
ACTGGATATGACCGAGTTAAACTCTTTACCAAGCTTTCAAGGATGATATGAGATATTTATTGACAACGGATAAACTGTGG
AGGAAAAGGAAGCCTCCTGTACCATTAGACTGGACTGAAGTTTCAGAGTCAAGAAATAAATTCAGGAGATCAACAAAATG
ATTCCACCTTAAGTTTAAAAGACTAACAGGTTCTAGATGTCAAAAGCTATGCACGTCTTTTTTCAAAGAGTATTGAAGCC
TTGAGAGTTCATCTAGCTGAAAAAGGTGATGGAGCTGAACTCATTTGGGACAAGGATGACCCATCAGCAATGGATTTTGT
TACATCTGCAGGAAACCTCTGGATGCATATTTTCAGTATGAATATGAAGAGTAGATTTGATATCAAATCAATGGCTGGAA
CTATCATTCCTGCAATAGCTACCACTAATGCAGTGATTGCTGGGCTGATAGTCCTGGATGGTTTGAAAATTTTATCAGGA
AAAAGAGATCAGTGTAGAATGATCTTTTTGAACAAACAGCCAAATCCAAGAAAGAAACTACTTGTGCCTTGTGCATTGGA
TCCTCCCAATCCTAATTGTTATGTTTGTGCCAGCAAGCCTGAGGTAACAGTCCACAAAGTCATAGTCCTTACATTACAGG
ATAAGATAGTGAAAGAAAAATTTGCCATAGTAGCACCAGATGTACAGATTGAAGATGGCAAAGGAACCATCCTGATATCT
TCAGAAGAGGGAGAAACAGAAGCTAATAATTATAAGAAGTTGTCAGAGTTTGGAATTAGAAGTGGCAAGCAGGTTTCAAG
CAGATGATTTCCTTCAGGATTATACATTACTGATCCATGTTCTTTATGGTGACGACCTAGAAAAAGAGGTGGAATTTGAA
GTTGTTGGAGATGTTCCTGAAAAAGTGGGGCCAAAGCAGGCAGAACAGTCAGCTAAAAACATCAGTAATGGCAGTGATGA
TGGGGCACAGCCATCTACATCAACAGCTCAAGATCAAGATGATGTGCGGATCGTTGATTCATATGAAGAAGCTCCTTCAG
GTAATACTGATGAAGTCACTGAGGAATACTCAACCTGGAAGAGAACGTTAGATGACAAAGAACATGTCAACACAAAGAGA
CCATGTACAGAACAGTCTGAAGAGCTAGATGACATTATAGCATTAGAT

Alignment

ORF - retro_mdom_1509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.97 %
• Parental protein coverage: 67.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QKTFPGCTIRNTPSEPIHCIVWAKYLFNQLFGEEDADQEVSPDRADPEAAWEPAEAEARARASNDDGDIK
          QKTF.GCTIRNTPSEPIHCIVWAKYLFN.LFGEEDADQEVSPDRADPE.AWEPAEAEARARASNDDGDIK
Retrocopy QKTFLGCTIRNTPSEPIHCIVWAKYLFN*LFGEEDADQEVSPDRADPETAWEPAEAEARARASNDDGDIK

Parental  RISTKEWAKSTGYDPVKLFTKL-FKDDIRYLLTMDKLWRKRKPPVPLDWTEV-QSQEINSGDQQNDSTLG
          .ISTKEWAKSTGYD.VKLFTKL.FKDD.RYLLT.DKLWRKRKPPVPLDWTEV.QSQEINSGDQQNDSTL.
Retrocopy CISTKEWAKSTGYDRVKLFTKL<FKDDMRYLLTTDKLWRKRKPPVPLDWTEV>QSQEINSGDQQNDSTLS

Parental  LKDQQVLDVKSYARLFSKSIETLRVHLAEKGDGAELIWDKDDPSAMDFVTSAANLRMHIFSMNMKSRFDI
          LKD.QVLDVKSYARLFSKSIE.LRVHLAEKGDGAELIWDKDDPSAMDFVTSA.NL.MHIFSMNMKSRFDI
Retrocopy LKD*QVLDVKSYARLFSKSIEALRVHLAEKGDGAELIWDKDDPSAMDFVTSAGNLWMHIFSMNMKSRFDI

Parental  KSMAGNIIPAIATTNAVIAGLIVLEGLKILSGKIDQCRTIFLNKQPNPRKKLLVPCALDPPNPNCYVCAS
          KSMAG.IIPAIATTNAVIAGLIVL.GLKILSGK.DQCR.IFLNKQPNPRKKLLVPCALDPPNPNCYVCAS
Retrocopy KSMAGTIIPAIATTNAVIAGLIVLDGLKILSGKRDQCRMIFLNKQPNPRKKLLVPCALDPPNPNCYVCAS

Parental  KPEVTVKLNVHKVTVLTLQDKIVKEKFAMVAPDVQIEDGKGTILISSEEGETEANNYKKLSEFGIRNG-S
          KPEVTV....HKV.VLTLQDKIVKEKFA.VAPDVQIEDGKGTILISSEEGETEANNYKKLSEFGIR.G.S
Retrocopy KPEVTV----HKVIVLTLQDKIVKEKFAIVAPDVQIEDGKGTILISSEEGETEANNYKKLSEFGIRSG>S

Parental  RLQADDFLQDYTLLINVLHSDDLEKDVEFEVVGDAPEKVGPKQAEQSAKNISNGSDDGAQPSTSTAQDQD
          R.QADDFLQDYTLLI.VL..DDLEK.VEFEVVGD.PEKVGPKQAEQSAKNISNGSDDGAQPSTSTAQDQD
Retrocopy RFQADDFLQDYTLLIHVLYGDDLEKEVEFEVVGDVPEKVGPKQAEQSAKNISNGSDDGAQPSTSTAQDQD

Parental  DVLIVDSDEEAPSSNTADVTEEDSARKRKLDDKEHVNAKRPRTEQSEELDDIIALD
          DV.IVDS.EEAPS.NT..VTEE.S..KR.LDDKEHVN.KRP.TEQSEELDDIIALD
Retrocopy DVRIVDSYEEAPSGNTDEVTEEYSTWKRTLDDKEHVNTKRPCTEQSEELDDIIALD

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	324.81 RPM
SRP007412_cerebellum	0.00 RPM	297.73 RPM
SRP007412_heart	0.00 RPM	119.01 RPM
SRP007412_kidney	0.00 RPM	243.61 RPM
SRP007412_liver	0.00 RPM	204.42 RPM
SRP007412_testis	0.00 RPM	486.96 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1509 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1509 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011975	3 retrocopies	retro_chof_1034, retro_chof_548, retro_chof_848,
Myotis lucifugus	ENSMLUG00000003047	1 retrocopy	retro_mluc_286,
Monodelphis domestica	ENSMODG00000011934	1 retrocopy	retro_mdom_1509 ,
Pongo abelii	ENSPPYG00000009837	1 retrocopy	retro_pabe_304,
Rattus norvegicus	ENSRNOG00000021113	1 retrocopy	retro_rnor_939,
Sus scrofa	ENSSSCG00000002876	1 retrocopy	retro_sscr_941,