RetrogeneDB ID: retro_amel_1902

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195455.1:22651..23408(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZCCHC4
• Ensembl ID: ENSAMEG00000018120
• Aliases: None
• Description: zinc finger, CCHC domain containing 4 [Source:HGNC Symbol;Acc:22917]

Sequence

>retro_amel_1902
CAGTTTTATGTGAAAGATAGTTTTTGCCATTATACCTTGTTTAACCATCACATCTTTGATGGGAAGTCTGCCTTCGAAGT
ATGCAGAACATGTTTACAGGAAAATAAAGGTGAGGGAATCATTATGGTGACAGGTCCTCCTTTTGGTGGTTTTGCTGAAC
CTCCAGTTGTTACATTCAAGAAATAAATTATGTGGAAAGAAGATCAAGACCAAGAAGAACTACCCATATTCTGAATTTTC
CCCTCTTTTTTGAAGTCCAACTTTATCCGTTTTTTCCAAGCTTCTGCATGCTGAATTACCAGATAGATTATGATAATCAT
GAGCTTTATACACATGGAAAGACAGGTTGAAAACAGTCTTCTGTGCATATTTTCACCAATATTCTACCCAGCAAAATAAT
CCTTCCTATTGAAGAAGAGTACAGATTTTGCCTCTGTGCTAATGATGTTTCCCTAGAAAATCAACACCATGAGCACTGCA
ATTCTTGCACCTCCAAGATGGCAAGAATGGAACCACTGCTTTGTCTGCATAAAGTGTGTAAAACCTTCCTGATTCCACTA
TAGCATTTGCAGTCACTGTGCCCTTCCAGATCATTCTCATAGGGGCCCCCAAATAGCTGTTTTATTTGTGGTGAATTAGA
TAATAAAAGTAGTACTTGCTCTAACATCTCTACATCTAAAAAAGTGAACAAAGCTGTCAGCAAGCAGAAGCAAAGAAAAG
TAATAAGATGAAAATGGAGACCACTAAAGGACAATCC

Alignment

ORF - retro_amel_1902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.83 %
• Parental protein coverage: 95.24 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QFYMEDSFCHYNMFNHHFFDGKAALEVCRTFLQEDKGEGVIMVTDPPFGGLVEPLAVTFKKLIAMWKEGQ
          QFY..DSFCHY..FNHH.FDGK.A.EVCRT.LQE.KGEG.IMVT.PPFGG..EP..VTFKK.I.MWKE.Q
Retrocopy QFYVKDSFCHYTLFNHHIFDGKSAFEVCRTCLQENKGEGIIMVTGPPFGGFAEPPVVTFKK*I-MWKEDQ

Parental  SQDSSHKELPIFWI-FPYFFESRIRQFFPSFCMLDYQVDYDNHALYKHGKTGRKQSPVRIFTNIPPNKII
          .Q.....ELPIF.I.FP.FFE.....FFPSFCML.YQ.DYDNH.LY.HGKTG.KQS.V.IFTNI.P.KII
Retrocopy DQE----ELPIF*I<FPLFFEVQLYPFFPSFCMLNYQIDYDNHELYTHGKTG*KQSSVHIFTNILPSKII

Parental  LPREEGYRFCALCQRYVSLENQHCEHCNSCTSK-DGR-KWNHCFLCKKCVKPSWIHCSICSHCALPDHSC
          LP.EE.YRFC.LC...VSLENQH.EHCNSCTSK.DG...WNHCF.C.KCVKPS..H.SICSHCALPDHS.
Retrocopy LPIEEEYRFC-LCANDVSLENQHHEHCNSCTSK<DGK<EWNHCFVCIKCVKPS*FHYSICSHCALPDHSH

Parental  GGPK-DGCFICGELDHKRSTCPKIATSKKVNKAVRKQKQR-KSSKMKMGTTKGQS
          .GP....CFICGELD.K.STC..I.TSKKVNKAV.KQKQR.KS.KMKM.TTKGQS
Retrocopy RGPQ<NSCFICGELDNKSSTCSNISTSKKVNKAVSKQKQR<KSNKMKMETTKGQS

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_1902 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1902 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	ENSAMEG00000018120	1 retrocopy	retro_amel_1902 ,
Myotis lucifugus	ENSMLUG00000004225	1 retrocopy	retro_mluc_1360,
Mustela putorius furo	ENSMPUG00000016727	1 retrocopy	retro_mputfur_1568,