RetrogeneDB ID: retro_amel_478

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192466.1:1954001..1954451(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC9
• Ensembl ID: ENSAMEG00000016933
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 9 [Source:HGNC Symbol;Acc:19123]

Sequence

>retro_amel_478
GAAGACATTCAAGAGTTTGGAAAGATATACAAAGGTTCTGAGGAAGAGCTGGCAATATTAAACAAGCCTATCTAAACTTC
AAGAGTGACACAGATCAGATCACACAGTCTATGCTGGATGTGCAGTATGCTGAGGAACCCAGGATATGGAACCTCATTCT
GCAAACCAGTCACACCAGAGAGATCCTATCCTATAATGCCTTTGTCAAAGAATCAAAGCAAAAGATGAATGCAAGGGAAA
GGATGGCCCAGGAAGAGTCTAAAGATCAGAAATGACCTGGAAGGGGCTGGGGAGCTTGATGAAAAAAGAGGTGGATAATC
TGAAACCAGTGTTCAAAGCAGGCAAAAGGATGGGCAATAGGAAATGGACAATATCCTGGCTCAAATGGAATCAAAGTACT
ACAAACCTTCCAACGTAGGAGAGGAAAGCACTTTCAAAAAAGAAAATAAA

Alignment

ORF - retro_amel_478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 57.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EDIQAFEKTYKGSEEELA-DIKQAYLDFKGDMDQIMESVLCVQYTEEPRIRNIIQQAIDAGEIPSYNAFV
          EDIQ.F.K.YKGSEEELA..IKQAYL.FK.D.DQI..S.L.VQY.EEPRI.N.I.Q.....EI.SYNAFV
Retrocopy EDIQEFGKIYKGSEEELA<NIKQAYLNFKSDTDQITQSMLDVQYAEEPRIWNLILQTSHTREILSYNAFV

Parental  KESKQKMNARKRRAQEEAKE-AEISRKELG--LDEGVDNLKAI-IQSRQKDRQKEMDNFLAQMEAKYCKP
          KESKQKMNAR.R.AQEE.K...E...K.LG......VDNLK....QSRQKD.Q.EMDN.LAQME.KY.KP
Retrocopy KESKQKMNARERMAQEESKD<SEMTWKGLGSLMKKEVDNLKPV<VQSRQKDGQ*EMDNILAQMESKYYKP

Parental  KRGGKKTPLKKEKK
          ...G.....KKE.K
Retrocopy SNVGEESTFKKENK

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_478 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_478 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016933	1 retrocopy	retro_amel_478 ,
Felis catus	ENSFCAG00000004448	1 retrocopy	retro_fcat_1310,
Homo sapiens	ENSG00000213551	2 retrocopies	retro_hsap_1358, retro_hsap_2448,
Gorilla gorilla	ENSGGOG00000015046	3 retrocopies	retro_ggor_1058, retro_ggor_1499, retro_ggor_1524,
Myotis lucifugus	ENSMLUG00000004539	3 retrocopies	retro_mluc_699, retro_mluc_700, retro_mluc_955,
Mustela putorius furo	ENSMPUG00000003792	1 retrocopy	retro_mputfur_727,
Nomascus leucogenys	ENSNLEG00000016595	1 retrocopy	retro_nleu_1394,
Otolemur garnettii	ENSOGAG00000003496	2 retrocopies	retro_ogar_1730, retro_ogar_1740,
Pongo abelii	ENSPPYG00000002343	2 retrocopies	retro_pabe_1126, retro_pabe_1799,
Pan troglodytes	ENSPTRG00000034219	2 retrocopies	retro_ptro_1414, retro_ptro_931,
Ictidomys tridecemlineatus	ENSSTOG00000028067	1 retrocopy	retro_itri_413,
Tarsius syrichta	ENSTSYG00000011504	1 retrocopy	retro_tsyr_39,