RetrogeneDB ID: retro_mdom_573

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:352422288..352423478(-)
• Located in intron of: ENSMODG00000008425

Retrocopy information

• Ensembl ID: ENSMODG00000008409
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000029494
• Aliases: None
• Description: None

Sequence

>retro_mdom_573
GTGCTTCCGAGTAAAATGGATGGTCAAGCGGGGGAGAAGACTGAGCCTAATCTCGTGTCGCACGAGCAGATTAAAAAGGC
TACAGAAGCTTTGTTGAGTTATACAAAGAAGAAACAAAATGATAATACATTACTTTTGAATGAGAACGAGAATGTGTTTT
TAATGGTGACATTATGGAAAATTCCCCCAAAGGGAAAAGAAATCAAAATCCCTTTGCCACACGGTATCAGGTCTGATTCA
AAAGACATATGCTTATTTACCAAGGATGAATCCAATTTAACTTCAGAACAGACAGAACATTTCTATAAGCAGCTTTTGAA
AAAGAAGGGAATTACAAGCATTACTGAGGTCATCCCTTATAAAAGATTAAAACAAGAATATAAACCTTATGAAGCCAAGC
GGCGCCTTTTGAATAGTTTTGACCTTTTTCTTGCTGATCAAAGAATTAGACGACTTTTGCCCTCACACATAGGAAAGCAT
TTCTATCGAAGAAAGAGAGTACCTCTAGCAGTAGACCTCACGACCCAAAATTTGTTGGAACACATCAATAAGATTGTCCA
GGGAACTACATTGACTGTCACTAATCATGGTTGTTGCAATACAACACGTGTGGGTCACACTGGAATGCCTGTAGATCATC
TAGTAGAAAATACTGTTGCTGCTATAAAAGTGCTTTCAGAAAAACTGCCAATGAAGTGGGAGAGTGTAAAAATTCTACAC
CTGAAAACAGAAAAATCTCTTTCCCTTCCAATCTTTTCTTCATTTGTCTCCCATTTGGGGACTCATAAGAAAACTAAGAA
GCAAAATCAAGGCAAAAAAGTGACCTCGAAGCCTGATCAAAATGCAGTGAGGCCTGATGGTGAGGGAAATTTGGAAGGTC
ATGGGCTTGAGGCCACAAAGGATGGCAAAACAGAACCTGACTCTGAGGATGAGATTCCACAGCTAGTTCCAATTCAAGCA
ACATCTCCTCAAAAGTGTCCAGAGAAAATAGCCCTAATTAAGGAGTCTACAGGAGAGAACCTCAGCCCTGAAACACCACA
AGCTAAAACTCGTGGTAAAAAGAGAAAAGCCTCCATGGCTCTGGAGACTTCAAAACAGATTAAGAAAGGTTCCACACAAT
TGAAGAAGACTCCAACCACTGGCAAAGTAAGAAGCCAAGGACCCATCCCTAAGAAAACACAGAAAGAAAA

Alignment

ORF - retro_mdom_573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.25 %
• Parental protein coverage: 91.71 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLPSRKMGGLADEKTKPQLVSHEEIKKATEDLLRYRKNKPNANPMLMSEDENMFLLVTLWKIPPEGKEIR
          .LPS.KM.G.A.EKT.P.LVSHE.IKKATE.LL.Y.K.K.N.N..L..E.EN.FL.VTLWKIPP.GKEI.
Retrocopy VLPS-KMDGQAGEKTEPNLVSHEQIKKATEALLSYTKKKQNDNTLLLNENENVFLMVTLWKIPPKGKEIK

Parental  IPLPHGIRPDSKDICLFTKDDPNLTSEETEIFYKQLFQKKGITSITEIIPFTRLKRQFKTYKTMRRLVSS
          IPLPHGIR.DSKDICLFTKD..NLTSE.TE.FYKQL..KKGITSITE.IP..RLK...K.Y...RRL..S
Retrocopy IPLPHGIRSDSKDICLFTKDESNLTSEQTEHFYKQLLKKKGITSITEVIPYKRLKQEYKPYEAKRRLLNS

Parental  FDLFLADQRITRLLFSHLGKLFVRRKKVPLAVNLSHRNLSQHINRIVQGTTLTVTNQGSLNTTRVGHIGM
          FDLFLADQRI.RLL.SH.GK.F.RRK.VPLAV.L...NL..HIN.IVQGTTLTVTN.G..NTTRVGH.GM
Retrocopy FDLFLADQRIRRLLPSHIGKHFYRRKRVPLAVDLTTQNLLEHINKIVQGTTLTVTNHGCCNTTRVGHTGM

Parental  PVDHLVENIVAAIDVLSEKLPEKWDSVKFLHLKTEKSLSIPIFPSFDSHLDSPQKSENQKQSKKVSFKPA
          PVDHLVEN.VAAI.VLSEKLP.KW.SVK.LHLKTEKSLS.PIF.SF.SHL....K...Q.Q.KKV..KP.
Retrocopy PVDHLVENTVAAIKVLSEKLPMKWESVKILHLKTEKSLSLPIFSSFVSHLGTHKKTKKQNQGKKVTSKPD

Parental  QTAVRPESECGLDGYKLEPAKESKTEPYSSKDEILQVVPVQGISPQKCLEKVALFEEYTGENFSPET-QA
          Q.AVRP..E..L.G..LE..K..KTEP..S.DEI.Q.VP.Q..SPQKC.EK.AL..E.TGEN.SPET.QA
Retrocopy QNAVRPDGEGNLEGHGLEATKDGKTEP-DSEDEIPQLVPIQATSPQKCPEKIALIKESTGENLSPETPQA

Parental  KTPGKKRKASIALDTAKQVNKSSTQLKTTPDVGK-DKKSRTHPQESPEEK
          KT.GKKRKAS.AL.T.KQ..K.STQLK.TP..GK..KK.RTHP.E..E.K
Retrocopy KTRGKKRKASMALETSKQIKKGSTQLKKTPTTGK<SKKPRTHP*ENTERK

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	10.01 RPM	0.00 RPM
SRP007412_cerebellum	4.24 RPM	0.00 RPM
SRP007412_heart	3.19 RPM	0.00 RPM
SRP007412_kidney	5.27 RPM	0.00 RPM
SRP007412_liver	9.57 RPM	0.00 RPM
SRP007412_testis	8.25 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_573 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_573 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018865	2 retrocopies	retro_cfam_1937, retro_cfam_691,
Choloepus hoffmanni	ENSCHOG00000010827	2 retrocopies	retro_chof_1617, retro_chof_852,
Callithrix jacchus	ENSCJAG00000008375	1 retrocopy	retro_cjac_2154,
Cavia porcellus	ENSCPOG00000010630	3 retrocopies	retro_cpor_1262, retro_cpor_276, retro_cpor_822,
Loxodonta africana	ENSLAFG00000013664	1 retrocopy	retro_lafr_364,
Myotis lucifugus	ENSMLUG00000000784	1 retrocopy	retro_mluc_1309,
Monodelphis domestica	ENSMODG00000029494	2 retrocopies	retro_mdom_1240, retro_mdom_573 ,
Otolemur garnettii	ENSOGAG00000015151	1 retrocopy	retro_ogar_2604,
Rattus norvegicus	ENSRNOG00000048608	1 retrocopy	retro_rnor_2771,
Sarcophilus harrisii	ENSSHAG00000016705	1 retrocopy	retro_shar_836,