RetrogeneDB ID: retro_amel_444

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192446.1:1025257..1025971(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIH1D2
• Ensembl ID: ENSAMEG00000004081
• Aliases: None
• Description: PIH1 domain containing 2 [Source:HGNC Symbol;Acc:25210]

Sequence

>retro_amel_444
CCAGCTCCCCAGTCAGCCACTCATCCAGTACCTGTAAGTGCTGGCCAACCACAAGATAGGTCTGAGACATCAGATGTGTA
CATGGTTGTTGATGTCACCTACAATGCTGGTGTTCTCCAGGTGGAGAAAAGCACCAGGTGCAAAAAGATCACTTAATATG
GATGGCCATGAAATGCATTGAGGACAACTCCAATTTACTCTCTCACATTCTTATAGTCTTACTAAATTTAGAAGAAAAGG
AAACACCCAAAGGATGAAACAAAACCTGACCAGAATGCAAACCGACCCCATGGGTTTAAGAGAGAAAACAGAGAAGAACT
GACCCTTGAGTGGATTAGAAATGGTAGTGTGAGCAATCCAGGTCCCTTTCCTCAACTTTTACTGCCAAGAGACCAAGTTT
TAAGCAAAACAAGGTATCTGACGGAAGATATTTCCAGTACAGAGATCCAGGTGGAGATGAAGAGATCAGCCTATGAATTA
AAAATTGTGGCTGCTCAGACTGAGAAACCCCTGAAAATTGACCTAGAAGTTAAATCACCTGATAGTAATTCAGTATGTCT
CTGTGACCTTAGTATTTCTGAGGATGATTTATTGATCGAGGTCTCAGAGAAGTACAGATTACATCTGAATCTTCCAGAAT
CTGTGCATACTGAAATGACTACAGCAAAATTTATCAAAGAGAAAGCTACATTAATCATCACAATGCCGCTGGTG

Alignment

ORF - retro_amel_444 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.6 %
• Parental protein coverage: 75.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PAPQSTTHPVPLSVGRPEDMSETSDVYTVIDVAYNPDVLQA-AEKDQVKKDQLIRMAMKCIEE-QFQFTL
          PAPQS.THPVP.S.G.P.D.SETSDVY.V.DV.YN..VLQ...EK.QV.KD.LI.MAMKCIE..Q.QFTL
Retrocopy PAPQSATHPVPVSAGQPQDRSETSDVYMVVDVTYNAGVLQV<GEKHQVQKDHLIWMAMKCIED<QLQFTL

Parental  SHFYSITKFRIKGSIQRMKQNLMGMQAD-PTNLREKMRKEELTLEQI-SSTASNPDHF-QLLLPKGEVSS
          SH.YS.TKFR.KG..QRMKQNL..MQ.D.P.......R.EELTLE.I.....SNP..F.QLLLP...V.S
Retrocopy SHSYSLTKFRRKGNTQRMKQNLTRMQTD<PHGFKRENR-EELTLEWIRNGSVSNPGPFPQLLLPRDQVLS

Parental  KTRCLIEEISSTEIQVEMKEPAYELKIVADQNEKPLEIEIKVELPGINSVSLCELSVSEDDLLIEVSEKY
          KTR.L.E.ISSTEIQVEMK..AYELKIVA.Q.EKPL.I...V..P..NSV.LC.LS.SEDDLLIEVSEKY
Retrocopy KTRYLTEDISSTEIQVEMKRSAYELKIVAAQTEKPLKIDLEVKSPDSNSVCLCDLSISEDDLLIEVSEKY

Parental  RLHLNLPESVHTEMTTAKFIKEKATLIITMPLV
          RLHLNLPESVHTEMTTAKFIKEKATLIITMPLV
Retrocopy RLHLNLPESVHTEMTTAKFIKEKATLIITMPLV

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_444 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_444 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004081	1 retrocopy	retro_amel_444 ,
Felis catus	ENSFCAG00000000608	1 retrocopy	retro_fcat_236,
Pteropus vampyrus	ENSPVAG00000009619	1 retrocopy	retro_pvam_1235,