RetrogeneDB ID: retro_mdom_125

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:87760615..87762148(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000008634
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: P4HB
• Ensembl ID: ENSMODG00000003000
• Aliases: None
• Description: prolyl 4-hydroxylase, beta polypeptide [Source:HGNC Symbol;Acc:8548]

Sequence

>retro_mdom_125
GCTAACAACTGCGCTCTGCTCTCTCTCGCCCTGGCAGTGTCTACTGAAGTCGCAGATCCTCCTCAAACCAAGGAGGATGA
AGACGATTACGTCCTGGTCTTAAATAATGGCAACATCAATGAGGCACTGAGCACCTATGAATATCTCTTGGTGTTCTTCC
ATGCTCCTTGGTGTCTTCCCTGTCGAGATTTGGCGCCTGAGTATGCCAAGGCAGCGGAACAGTTGAAATCTGAGAGATCT
ATCAAGTTAGCCAAAATAGATGCCACTCAAGAACATGGTCTAGCACGGCAGTTTAGCATTCGACTCTACCCTACTATCAA
GTTATTTAAGCATGGAGATACATCTTCTCCTAAGGAGTATACGGAAGGCAGAGATGCTGAAGATATCGTGAAATGGATGC
AGCTACAACTCCAGCCCGCTGTCATTATCTTGGAAGATGTCCCTACTGTAGAGTCTTTAGTGGATTCCAATGAACTTGTT
GTTTTAGGCATATTCAAAGATGCTCAGTCGGATAATGTTAAGAATTTCACACTGGCTGCAGAGTCCATCGATGGTATCCC
ATTCGGAATCACTTACAACAACGAGGCGTTTTCGAAATATCAACTGGAGAAAGATAGCATTATCCTCTTTAAGAAGTTTG
ATGAAGGTCGAAACAACTTTCATGGAGAGATTTCAAAAATGAACTTAATAAATTTTGTTCATAACCACTGGCTGCCCTTG
GTCACCGAGTACAATGAACATACTGCCCCAAGGATTTTTGAAAGTCAGGTGAAAAATCATCTGCTAATATTCTTGCAAAA
GAGCAATAATGACTTTGAGGACAAAATTAGCAACTTCAAAAAAGCGGCTGAAAGTTACAGGGGGAAAATCCTATATATCC
TCATTGATATTGAATTCAGTGACAACAAGGGGATCCTTAAATTCTTTAGCCTGAAAGAAGAAGAGTGCCCAACGATGCGT
CTCATTAGTATGGAAAGTGACATGACCAAGTACAAGCCAGAGACAAATGAATTAACGATAGAAAAGATAGACGAATTCTG
TAAAAAGTATTTAGAGGAAAAATCCAAGTCCCATCTGATGAGCCAAGATGTGCCTGATGACTGGGATAAAAAGCCTGTTA
AAATATTGGTTGGGAAAAACTTTGAAAAAGTTGCTTTCGATGAGAAAAAGAACGTCTTTGTGAACTTCTATGCTCCTTGG
TGTAGTCAGTGCATAGGGATAGCTCCCATTTGGGATAAACTGGGAGATGTTTACAAGGATCATCAAGATATAGTCATTGC
TAAGATGGACTCATCAGTTAATGAAGTTGATTCAATTACAGTCCATAATTTCCCCACACTGATATACTTCCCTGCAGGTA
CCGACAGAAAAATCATTGAATACCATGGGGCATGGACTCTAGAAAATTTCAGAAAGTTCCTAGACAGCGGTGACTATGAT
AGACCAAAGAAAATAAGTGGCTTAGAGGTCCTAGAAGAAACTGAAGAAATGGAATCACAAGATAGGAAAGAGAGAGGACA
AAGAACTCATTCT

Alignment

ORF - retro_mdom_125 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.87 %
• Parental protein coverage: 97.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NRVLLCLALAVMAGVRADAPK----EEDDVLVLNKSNFGEALKSYEYLLVEFYAPWCGHCKALAPEYAKA
          N..LL.LALAV...V.AD.P.....E.D.VLVLN..N..EAL..YEYLLV.F.APWC..C..LAPEYAKA
Retrocopy NCALLSLALAVSTEV-ADPPQTKEDEDDYVLVLNNGNINEALSTYEYLLVFFHAPWCLPCRDLAPEYAKA

Parental  AGKLKAEGSKIRLAKVDATEESDLARQYGVRGYPTIKFFKNGDTTSPKEYTAGREAEDIVNWLKKRTSPA
          A..LK.E.S.I.LAK.DAT.E..LARQ...R.YPTIK.FK.GDT.SPKEYT.GR.AEDIV.W......PA
Retrocopy AEQLKSERS-IKLAKIDATQEHGLARQFSIRLYPTIKLFKHGDTSSPKEYTEGRDAEDIVKWMQLQLQPA

Parental  VTVLRDVAAAESLVDSSEVAVIGLFKDVDSEFVKQFTLAAESIDDIPFGISSSNDVYSKYQMDKDGIILL
          V..L.DV...ESLVDS.E..V.G.FKD..S..VK.FTLAAESID.IPFGI...N...SKYQ..KD.IIL.
Retrocopy VIILEDVPTVESLVDSNELVVLGIFKDAQSDNVKNFTLAAESIDGIPFGITYNNEAFSKYQLEKDSIILF

Parental  KKFDEGRNNYDGEITKENLMDFVNYHRLPLVIEFTEQTAPKIFGGEIKTHILLFLPKSVSDYDDKLSNFK
          KKFDEGRNN..GEI.K.NL..FV..H.LPLV.E..E.TAP.IF....K.H.L.FL.KS..D..DK.SNFK
Retrocopy KKFDEGRNNFHGEISKMNLINFVHNHWLPLVTEYNEHTAPRIFESQVKNHLLIFLQKSNNDFEDKISNFK

Parental  KAAESFKGKILFIFIDSDHTDNQRILEFFGLKKEECPAVRLITLEEEMTKYKPESDELTAEKIKEFCDRF
          KAAES..GKIL.I.ID....DN..IL.FF.LK.EECP..RLI..E..MTKYKPE..ELT.EKI.EFC...
Retrocopy KAAESYRGKILYILIDIEFSDNKGILKFFSLKEEECPTMRLISMESDMTKYKPETNELTIEKIDEFCKKY

Parental  LEGKVKPHLMSQDLPDDWDKQPVKVLVGKNFEEVAFDEKKNVFVEFYAPWCGHCKQLAPIWDKLGETYKD
          LE.K.K.HLMSQD.PDDWDK.PVK.LVGKNFE.VAFDEKKNVFV.FYAPWC..C...APIWDKLG..YKD
Retrocopy LEEKSKSHLMSQDVPDDWDKKPVKILVGKNFEKVAFDEKKNVFVNFYAPWCSQCIGIAPIWDKLGDVYKD

Parental  HESIVIAKMDSTANEVEAVKVHSFPTLKFFPASADRTVIDYNGERTLEGFKKFLESGGQDGAGDDDDLED
          H..IVIAKMDS..NEV....VH.FPTL..FPA..DR..I.Y.G..TLE.F.KFL.SG..D.......LE.
Retrocopy HQDIVIAKMDSSVNEVDSITVHNFPTLIYFPAGTDRKIIEYHGAWTLENFRKFLDSGDYDRPKKISGLEV

Parental  LEEAEEPDMEE
          LEE.EE.....
Retrocopy LEETEEMESQD

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	0.72 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	12764.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_125 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_125 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000003000	2 retrocopies	retro_mdom_125 , retro_mdom_673,
Sarcophilus harrisii	ENSSHAG00000011040	1 retrocopy	retro_shar_29,