RetrogeneDB ID: retro_mdom_1240

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:61896668..61897602(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_mdom_1240
TGCTTCTTTACCAAGGATGAATCCAATTTAACTTCAGAACAGACAGAACATTTCTATAAGCAGCTTTTGAAAAAGAAGGG
AATTCCAAGCATTCCTGAGGTCATCCCTTATAAAAGATTAAAACAAGAATATAAACTTTATGAAGCCAAGCGGCGCCTTT
TGAGTAGTTTTGACCTTTTTCTTGTTGATCAAAGAATTAGACGACTTTTACCCTCACACATAAGAAAGTAATTCTATCGA
AGAAAGAAAGTACCTCTAGCAGTAGACCTCACAACTCAAATGTTGGAACACATCAATAAGACTGTCCAGGGAACTACACT
GATGGTCACTAATCATGGTTGTTGCAATACATGTGTGGGTCACACTAGAATGCCTGTAGATCATCGAGTAGAAAATACTG
TTGCTGCTATAAAGGTGCCTTCAGAAAAGCTGCCAATGAAGTGGGAGAGTGTAAAAATTCTACACCTAAAACAAAAAAAA
TCTCTTTCCCTTCCAATGTTTTCTTCATTTGTCTCCTCTTTGGGGACTCATCAGAAAACTAAGAATCAAAATCAAGGCAA
AAAGTGACCTTGAAGCCTGCTCAAACTACAGAGAAGGCTGATGGTGAGGGTAATTTGGAGGGTCATGAGCTTGAGGCCAC
AAAGGATGGCAAAACAGAACCTGACTCTGAGGATGAGATTCCACAGCTAGTTCCAATTCAAGCAACATCTCCTCAAAAGT
GCCCAGAGAAAGTAGCCCTAATTAAGAAGTCTACAGGAGAGAGCCTCAGTCCTGAAACAGTACAAGCTTAAACTCTTGGT
AAAAAGAGAAAAGCCTCCATGGCTCTGGAGACTCCAAAACAGATTAAGAAAGGTTCCACACCATTGAAGAAGACTCCAGC
CACTGGCAAAGTAAGAAGCCAAGGACCCATCCCTAAGAAAACACAGAAAGAAAA

Alignment

ORF - retro_mdom_1240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.83 %
• Parental protein coverage: 72.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CLFTKDDPNLTSEETEIFYKQLFQKKGITSITEIIPFTRLKRQFKTYKTMRRLVSSFDLFLADQRITRLL
          C.FTKD..NLTSE.TE.FYKQL..KKGI.SI.E.IP..RLK...K.Y...RRL.SSFDLFL.DQRI.RLL
Retrocopy CFFTKDESNLTSEQTEHFYKQLLKKKGIPSIPEVIPYKRLKQEYKLYEAKRRLLSSFDLFLVDQRIRRLL

Parental  FSHLGKLFVRRKKVPLAVNLSHRNLSQHINRIVQGTTLTVTNQGSLNTTRVGHIGMPVDHLVENIVAAID
          .SH..K.F.RRKKVPLAV.L....L..HIN..VQGTTL.VTN.G..NT..VGH..MPVDH.VEN.VAAI.
Retrocopy PSHIRK*FYRRKKVPLAVDLTTQML-EHINKTVQGTTLMVTNHGCCNTC-VGHTRMPVDHRVENTVAAIK

Parental  VLSEKLPEKWDSVKFLHLKTEKSLSIPIFPSFDSHLDSPQKSENQKQSK-KVSFKPAQTAVRPESECGLD
          V.SEKLP.KW.SVK.LH.....SLS.P.F.SF.S.L...QK..NQ.Q.K.KV..KPAQT......E..L.
Retrocopy VPSEKLPMKWESVKILHXXXXXSLSLPMFSSFVSSLGTHQKTKNQNQGK<KVTLKPAQTTEKADGEGNLE

Parental  GYKLEPAKESKTEPYSSKDEILQVVPVQGISPQKCLEKVALFEEYTGENFSPET-QAKTPGKKRKASIAL
          G..LE..K..KTEP..S.DEI.Q.VP.Q..SPQKC.EKVAL....TGE..SPET.QA.T.GKKRKAS.AL
Retrocopy GHELEATKDGKTEP-DSEDEIPQLVPIQATSPQKCPEKVALIKKSTGESLSPETVQA*TLGKKRKASMAL

Parental  DTAKQVNKSSTQLKTTPDVGK-DKKSRTHPQESPEEK
          .T.KQ..K.ST.LK.TP..GK..KK.RTHP.E..E.K
Retrocopy ETPKQIKKGSTPLKKTPATGK<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	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_1240 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1240 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,