RetrogeneDB ID: retro_amel_252

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192366.1:491195..491470(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC19
• Ensembl ID: ENSAMEG00000012255
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 19 [Source:HGNC Symbol;Acc:30528]

Sequence

>retro_amel_252
GCCAGTATGGTGGTAGCAGTTGGTCTGACCGCTACTGCGGCGGGATTTGCAGGCCATGATGTTTTGCCAGCCACGAACCA
TATGGAGCCTCAAGTAAAACAGGTTTTTCAAAGTCTACCAAAACTGCCTTCCGCAGGGGCTGTTGTATAGGCGGGTTTGA
ACCCCAAATGACAAAACGAGAAGCAGCATTATTACTAAGCGTAAACCCTCCTGCCACTAAAGGAAAAAGAAGAGATGCTC
ATTGATGAATTATGCTTTTAAATTACCCAGACGAG

Alignment

ORF - retro_amel_252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.97 %
• Parental protein coverage: 70.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASTVVAVGLTIAAAGFAGRYVLQAMKHMEPQVKQVFQSLPK-SAFSGGYYRGGFEPKMTKREAALILGIS
          AS.VVAVGLT..AAGFAG..VL.A..HMEPQVKQVFQSLPK..AF..G...GGFEP.MTKREAAL.L...
Retrocopy ASMVVAVGLTATAAGFAGHDVLPATNHMEPQVKQVFQSLPK<TAFRRGCCIGGFEPQMTKREAALLLSVN

Parental  PTANKGKIRDAHRRIMLLNHPDK
          P.A.KGK.RDAH..IMLLN.PD.
Retrocopy PPATKGKRRDAH**IMLLNYPDE

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_252 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_252 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 16 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012255	6 retrocopies	retro_amel_1087, retro_amel_155, retro_amel_252 , retro_amel_283, retro_amel_744, retro_amel_994,
Bos taurus	ENSBTAG00000023513	1 retrocopy	retro_btau_127,
Callithrix jacchus	ENSCJAG00000012795	10 retrocopies	retro_cjac_1008, retro_cjac_1192, retro_cjac_1364, retro_cjac_1430, retro_cjac_1550, retro_cjac_252, retro_cjac_2609, retro_cjac_2890, retro_cjac_3060, retro_cjac_914,
Cavia porcellus	ENSCPOG00000021198	1 retrocopy	retro_cpor_126,
Dasypus novemcinctus	ENSDNOG00000019067	1 retrocopy	retro_dnov_49,
Erinaceus europaeus	ENSEEUG00000006955	9 retrocopies	retro_eeur_221, retro_eeur_230, retro_eeur_309, retro_eeur_455, retro_eeur_48, retro_eeur_511, retro_eeur_596, retro_eeur_74, retro_eeur_94,
Echinops telfairi	ENSETEG00000006897	7 retrocopies	retro_etel_1071, retro_etel_1222, retro_etel_1559, retro_etel_275, retro_etel_384, retro_etel_81, retro_etel_821,
Ficedula albicollis	ENSFALG00000008296	1 retrocopy	retro_falb_28,
Felis catus	ENSFCAG00000010591	7 retrocopies	retro_fcat_1250, retro_fcat_1481, retro_fcat_1603, retro_fcat_1837, retro_fcat_475, retro_fcat_511, retro_fcat_982,
Gallus gallus	ENSGALG00000008852	1 retrocopy	retro_ggal_17,
Loxodonta africana	ENSLAFG00000001910	5 retrocopies	retro_lafr_48, retro_lafr_515, retro_lafr_611, retro_lafr_881, retro_lafr_929,
Microcebus murinus	ENSMICG00000010381	4 retrocopies	retro_mmur_1160, retro_mmur_225, retro_mmur_320, retro_mmur_728,
Myotis lucifugus	ENSMLUG00000006865	1 retrocopy	retro_mluc_84,
Mustela putorius furo	ENSMPUG00000002336	7 retrocopies	retro_mputfur_1099, retro_mputfur_1652, retro_mputfur_287, retro_mputfur_662, retro_mputfur_841, retro_mputfur_848, retro_mputfur_984,
Otolemur garnettii	ENSOGAG00000008754	11 retrocopies	retro_ogar_1214, retro_ogar_1334, retro_ogar_138, retro_ogar_1625, retro_ogar_1811, retro_ogar_2012, retro_ogar_2048, retro_ogar_2881, retro_ogar_301, retro_ogar_442, retro_ogar_718,
Tupaia belangeri	ENSTBEG00000015089	27 retrocopies	retro_tbel_1126, retro_tbel_1166, retro_tbel_1167, retro_tbel_1296, retro_tbel_1301, retro_tbel_1491, retro_tbel_1693, retro_tbel_1780, retro_tbel_2117, retro_tbel_2136, retro_tbel_2267, retro_tbel_2459, retro_tbel_266, retro_tbel_2830, retro_tbel_3233, retro_tbel_3303, retro_tbel_3556, retro_tbel_3716, retro_tbel_3814, retro_tbel_384, retro_tbel_3849, retro_tbel_3963, retro_tbel_4043, retro_tbel_42, retro_tbel_633, retro_tbel_833, retro_tbel_889,