RetrogeneDB ID: retro_shar_29

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834459.1:1301962..1303498(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000013721
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: P4HB
• Ensembl ID: ENSSHAG00000011040
• Aliases: None
• Description: prolyl 4-hydroxylase, beta polypeptide [Source:HGNC Symbol;Acc:8548]

Sequence

>retro_shar_29
AGCTGCGCTCTCCTTTTCCTAACCCTGGCCGTCTCCACCGAGGTCGCAGACACTCCTGAGACCGAAGAGGAGGATGATAA
TGTGCTGATCTTAAAAACGAGCAACTTCAATGAGGTGCTGGCCACCTGTGACTACCTCTTGGTGGACTTCTATGCCCCTT
GGTGTAAGCCCTGTAGAGATTTGATACCTGAGTTTTCCAAGGCAGCGGAACAATTGAAAGTCGAGAACTCTAATATCACA
TTGGCCAAAGTAGATGCCACTGAAGAGCACGATCTAGCAGAACAGTTTAACATTCGAGTGTTCCCTACTATCAAGTTATT
TAAAAATGGAGATGCATCTTTCTCTAAGGATTATACAAACGGCAGAGAAGCTAAGGATATTGTGGAATGGATGAAGAAAC
GAATCCAGCCCTCTGTCATTTTGCTGGAGGATGCTGCTGCTGCAGAGTCTTTAATGGTTTCCAATGAAGTTTTTGTTTTA
GGCTTATTCAAAGATGGTCAGTCCTCCAATGCTAAGAATTTCTCAGATGCTGCAGAGTACTTCGATAACATCCCATTTGG
AATGACTTTCACCGAAGACGTCTTCACCCAATATCAATTGGATAAAGATAGCATTATTCTTTTTAAGAAGTTTGATGAAG
GTCGAATCGACTTCGATGAAGAGATTACAAAAATGAATGTAGTAAATTTTGTCAATCACCACCAGCTGCCCTTGGTCATC
GAGTTCTCCGAGGAGACTGCCCCGAAGATTTTCGCAGGTCAGTTGAAAACACATTTATTATTGTTCATGCCCAAGAACAG
TCCGGATTATGAGGACAAAATGGACCAATTCAAAAAAGCAGCTGAAAGTTTCAGGGAGAAAATCCTATTTATCATCATCG
ATACCAACAACAATGACAACATGGGTATCCTTAATTTCTTTGGCTTGAGTCAAGAAGAGTGCCCAACAATGCGACTCATT
AGTATGGAGACTGAGATGGTCAAGTACAAGCCTGAGTCAGAAGAATTAACTACAGAGTCAATAGAGGAATTCTGTAGGCA
GTTTTTGGAGGGCAAATTCAACTTCCATTTGATAAGCCAAGATGTGCCTGATGACTGGGATAAAGGGCCTGTTAAAGTGT
TGGTTGGGAAGAACTTTGACAGTGTTGCTTTTGATCCAAGAACTAATGTCTTTGTGAACTTCTATGCCCCTTGGTGTGGT
CAGTGCAAAAAACTAGATCCCATTTGGGAAAAACTGGGAGAAGCTTACAAGGATCATGAAAATATAATCATTGCCAAGAT
GGACTCATCAGTTAATGAGGTAGATTCTGTTGTGGTCCACAGTTTTCCCACACAGAAGTACTTCCCTGCAGGTATTGGTA
GAAAAATCATTGAATACCATGGGGTAAGGACACTAGAAGGTTTCAAAAATTTCCTAGACAATGGTGGCCATGAGGGACTA
AGGGAAATAGGTCATTTAGAAGTCCTAGATGAAGCTGAAGAACTCGAGTTAGAAGATCAGAATGAACAACAACAAGATAA
TGCGAAAGATGAGAAA

Alignment

ORF - retro_shar_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.9 %
• Parental protein coverage: 98.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRALLCLALAVTAGVRADSP---EEEDDVLVLKKSNFEKALATYEYLLVEFYAPWCGHCKALAPEYAKAA
          S.ALL.L.LAV...V.AD.P...EE.D.VL.LK.SNF...LAT..YLLV.FYAPWC..C..L.PE..KAA
Retrocopy SCALLFLTLAVSTEV-ADTPETEEEDDNVLILKTSNFNEVLATCDYLLVDFYAPWCKPCRDLIPEFSKAA

Parental  GKLKAEGSKIRLAKVDATEESDLAQQYGVRGYPTIKFFKNGDTASPKEYTAGREAEDIVNWLKKRTSPAV
          ..LK.E.S.I.LAKVDATEE.DLA.Q...R..PTIK.FKNGD....K.YT.GREA.DIV.W.KKR..P.V
Retrocopy EQLKVENSNITLAKVDATEEHDLAEQFNIRVFPTIKLFKNGDASFSKDYTNGREAKDIVEWMKKRIQPSV

Parental  TVLTDVAAAESLVDSNEVAVIGLFKDLESELVKQFTLAAESIDDIPFGVSSNSDVYSKYQFDKDGIILLK
          ..L.D.AAAESL..SNEV.V.GLFKD..S...K.F..AAE..D.IPFG.....DV...YQ.DKD.IIL.K
Retrocopy ILLEDAAAAESLMVSNEVFVLGLFKDGQSSNAKNFSDAAEYFDNIPFGMTFTEDVFTQYQLDKDSIILFK

Parental  KFDEGRNNFEGEITKENLLTFVNYHRLPLVIEFTEQTAPKIFGGEIKTHILLFLPKSVSDYDDKLNNFKK
          KFDEGR..F..EITK.N...FVN.H.LPLVIEF.E.TAPKIF.G..KTH.LLF.PK...DY.DK...FKK
Retrocopy KFDEGRIDFDEEITKMNVVNFVNHHQLPLVIEFSEETAPKIFAGQLKTHLLLFMPKNSPDYEDKMDQFKK

Parental  AAESFKGKILFIFIDSDHTDNQRILEFFGLKKEECPAVRLITLEEEMTKYKPESDELTAEKIKEFCDRFL
          AAESF..KILFI.ID....DN..IL.FFGL..EECP..RLI..E.EM.KYKPES.ELT.E.I.EFC..FL
Retrocopy AAESFREKILFIIIDTNNNDNMGILNFFGLSQEECPTMRLISMETEMVKYKPESEELTTESIEEFCRQFL

Parental  EGKVKPHLMSQDLPDDWDKQPVKVLVGKNFEEIAFDEKKNVFVEFYAPWCGHCKQLAPIWDKLGETYKDH
          EGK...HL.SQD.PDDWDK.PVKVLVGKNF...AFD...NVFV.FYAPWCG.CK.L.PIW.KLGE.YKDH
Retrocopy EGKFNFHLISQDVPDDWDKGPVKVLVGKNFDSVAFDPRTNVFVNFYAPWCGQCKKLDPIWEKLGEAYKDH

Parental  ESIVIAKMDSTANEVEAVKVHSFPTLKFFPASADRTVIDYNGERTLEGFKKFLESGGLDGAGDDDDLEDL
          E.I.IAKMDS..NEV..V.VHSFPT.K.FPA...R..I.Y.G.RTLEGFK.FL..GG..G......LE.L
Retrocopy ENIIIAKMDSSVNEVDSVVVHSFPTQKYFPAGIGRKIIEYHGVRTLEGFKNFLDNGGHEGLREIGHLEVL

Parental  EEAEEPDMEEDDDQ
          .EAEE...E....Q
Retrocopy DEAEELELEDQNEQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_29 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 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 ,