RetrogeneDB ID: retro_amel_396

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192419.1:2149275..2149874(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000010582
• Aliases: None
• Description: None

Sequence

>retro_amel_396
ACTCTGTCCAGCCCGCAGCGTGCAGGTGGCCTGTGCCGAAGCGCCGGGGAAAGCCCTGGGGCACTGGGACCCAGAGCCGA
GGAACGGCCGCTGCAGACGCGGCCTGCACCTGCAAGTGGTCCCCCGTGGGCATGGGGTTCGGCTTCCTGGCCGTGACTGC
CAGCTAGGGGTTTGCACAAGGCCCTCAAATGGATGTCTTGATGCCCCAGAGTCAACTGCTCCTGAAGGGCTTTCAGAGCC
TGAAGGAGGGTGTGGCAGTGGAGTTGACCTTTAAGAAGTCCCCACCGGCCTGGAATCTCTTTGTGTCCCGGCCCTGGTGG
GGTATTCTGTACTGGGAGTGAGAGAGCGCCAAAAGGAGGAGCATGCAGAAGGATTATCAAAGGAAATCGGTGCTACAACT
ATGGAAGTCTAGACTATCAGGCCAAGGAAAGCAAGCTGCCATCCCACCCAGAAGTACCCTTTCTACCAGAGCTTCCGAGC
CCCGTGATGGCCTGGTGTCCACTGAAGGGTCCATAGAACCCTACTCACAGGCAAAGCCAGCCTACTTTCAGGAGGAAAAA
GAGATCCGCAGCTGGGCCCTGCTCCCAGAAGGCCAGAAT

Alignment

ORF - retro_amel_396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.44 %
• Parental protein coverage: 99.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SVSNQQFAGGCAKAPEEAPEDAARAAEEPQL-LHGAGICKWFNVRMGFGFLSMTARAGVALDPPVDVFVH
          ..S..Q.AGG......E.P......AEE..L....A..CKW..V.MGFGFL..TA..G.A..P..DV...
Retrocopy TLSSPQRAGGLCRSAGESPGALGPRAEERPL<ADAACTCKWSPVGMGFGFLAVTAS*GFAQGPQMDVLMP

Parental  QSKLHMEGFRSLKEGEAVEFTFKKS-AKGLESIRV-TGPGGVFCIGSERRPKGKNTQKRRSKGDRCYNCG
          QS.L...GF.SLKEG.AVE.TFKKS...GLES..V..GPGGVFC.GSER.PKG.....R..KG.RCYN.G
Retrocopy QSQLLLKGFQSLKEGVAVELTFKKS<PTGLESLCV<PGPGGVFCTGSERAPKG-GACRRIIKGNRCYNYG

Parental  GLDHHAKECKLPPQPKKCHFCQSISHMVASCPRK-AQQAPSSQGKPTYFREEEEEEIHSPALLPEAQN
          .LD..AKE.KLP..P.........S...A.CP.K.....P.SQ.KP.YF...EE.EI.S.ALLPE.QN
Retrocopy SLDYQAKESKLPSHPEVPFLPELPSPVMAWCPLK<GSIEPYSQAKPAYF--QEEKEIRSWALLPEGQN

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_396 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_396 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 20 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010582	2 retrocopies	retro_amel_396 , retro_amel_649,
Bos taurus	ENSBTAG00000040497	3 retrocopies	retro_btau_1150, retro_btau_1594, retro_btau_199,
Canis familiaris	ENSCAFG00000012488	2 retrocopies	retro_cfam_2049, retro_cfam_767,
Callithrix jacchus	ENSCJAG00000009796	5 retrocopies	retro_cjac_1468, retro_cjac_1784, retro_cjac_186, retro_cjac_2597, retro_cjac_33,
Cavia porcellus	ENSCPOG00000019646	1 retrocopy	retro_cpor_120,
Dasypus novemcinctus	ENSDNOG00000010710	5 retrocopies	retro_dnov_102, retro_dnov_1112, retro_dnov_2300, retro_dnov_690, retro_dnov_853,
Equus caballus	ENSECAG00000020267	1 retrocopy	retro_ecab_258,
Homo sapiens	ENSG00000131914	2 retrocopies	retro_hsap_2187, retro_hsap_2450,
Gorilla gorilla	ENSGGOG00000024918	2 retrocopies	retro_ggor_1526, retro_ggor_1732,
Myotis lucifugus	ENSMLUG00000010158	1 retrocopy	retro_mluc_1023,
Nomascus leucogenys	ENSNLEG00000009294	4 retrocopies	retro_nleu_204, retro_nleu_2300, retro_nleu_2896, retro_nleu_316,
Oryctolagus cuniculus	ENSOCUG00000000299	1 retrocopy	retro_ocun_19,
Otolemur garnettii	ENSOGAG00000003971	1 retrocopy	retro_ogar_481,
Pongo abelii	ENSPPYG00000001684	3 retrocopies	retro_pabe_1801, retro_pabe_2067, retro_pabe_2849,
Pan troglodytes	ENSPTRG00000000384	2 retrocopies	retro_ptro_1415, retro_ptro_1665,
Pteropus vampyrus	ENSPVAG00000017267	1 retrocopy	retro_pvam_110,
Rattus norvegicus	ENSRNOG00000038409	2 retrocopies	retro_rnor_2076, retro_rnor_2077,
Sus scrofa	ENSSSCG00000003557	1 retrocopy	retro_sscr_358,
Ictidomys tridecemlineatus	ENSSTOG00000004329	1 retrocopy	retro_itri_1647,
Tursiops truncatus	ENSTTRG00000005678	4 retrocopies	retro_ttru_1312, retro_ttru_1559, retro_ttru_481, retro_ttru_548,