RetrogeneDB ID: retro_mdom_394

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:380781515..380782224(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010276
• Aliases: None
• Description: None

Sequence

>retro_mdom_394
CTGAATACCAAAAGATTAAAGCAGAAAAGAAATGATTATAATAGAAAACAAGACCTTAAGGACCAGAATTCAGCAATTGG
AAATCAATGACCTTTCAAAATAGCAAGAATTAATAAAGCAAAGTCAAAAGACTGACAAAATAGAAGGAAACATATAATAT
CTCACTGATAAGGTGACAGGTCTGAAAAATAGAGGAAGGAGAGACAATTTGATAATCATTGGTCTACCTGAAAAGCCAAA
AATAAACAGAAACCTTGACACCATACTGCAAGAGATCATCAAAGAAAACTGCCCTGAAGTTCTTGAATAAAGGGGATGGG
GGGAAATAGACATTGAAAGAGTTCATAGAACACCCTCTCCACTAAATCCAAAAAAATAAAAAAATAAAAAAACAACTCCC
AGAAATGTAAATGCCAAATTCCAGAGCTTTCAAGCTAAGGAGAAAATTCTACAAGAAGCCAAAAATAGGAAATTCAGATA
CCAAGAAGCACCAATCAGGATCACACAAGACCTGGCAGACTCCACACTAAAGGACCACAAGGCCTAGAACACAATATTCA
TAAAGGCAAGAGATCTGGGTCTTCAACCAAGAATCAACTATCCATCAAAACTGACTATATACTTCCAGGGGAAAGTATGG
GCATTCAACAAAATAGAAGATTTCCAAGTATTTGTAAAGAAAAGACCAGAACTAAGTGGAAAGTTTGAT

Alignment

ORF - retro_mdom_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.25 %
• Parental protein coverage: 64.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQRKSDQKEKDDQKTKDEIQSLRTRIQQ---IESTRINKA-SQKINDLEENMKYLTEKVTDLENRGRRDN
          L..K.......D...K.........I.........RINKA.SQK....E.N..YLT.KVT.L.NRGRRDN
Retrocopy LNTKRLKQKRNDYNRKQDLKDQNSAIGNQ*PFKIARINKA>SQKTDKIEGNI*YLTDKVTGLKNRGRRDN

Parental  LRIIGLPKKPEINKNLDAILQEIIEENCPHDLE-QG-GKIEIERVHRTPSILNPQKTTPRNIIAKLKTLN
          L.IIGLP.KP.IN.NLD.ILQEII.ENCP..LE..G.G.I.IERVHRTPS.LN.................
Retrocopy LIIIGLPEKPKINRNLDTILQEIIKENCPEVLE*RGWGEIDIERVHRTPSPLNXXXXXXXXXTPRNVNAK

Parental  FSKFKRSQVREKIIQAVRKKQFRYLGILFSISQDLAASTLKDCKVDNMIFYKARELDLQQRITYPSKLMT
          F..F...Q..EKI.Q......FRY......I.QDLA.STLKD.K..N.IF.KAR.L.LQ.RI.YPSKL..
Retrocopy FQSF---QAKEKILQEAKNRKFRYQEAPIRITQDLADSTLKDHKA*NTIFIKARDLGLQPRINYPSKLTI

Parental  LFKGKVWSFGKIEDFPAFLKKRPDVKRKFN
          .F.GKVW.F.KIEDF..F.KKRP....KF.
Retrocopy YFQGKVWAFNKIEDFQVFVKKRPELSGKFD

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	0.95 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_394 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_394 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010276	1 retrocopy	retro_mdom_394 ,