RetrogeneDB ID: retro_amel_1232

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193074.1:600533..600970(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VBP1
• Ensembl ID: ENSAMEG00000009058
• Aliases: None
• Description: None

Sequence

>retro_amel_1232
ATGAACAGTTACCACAAGTATAAGTTTATGGAACTCAACCTTGCTCAAAGGAAAAGGAGCCTGAAAGGTCAAAATCCTGA
AATTAAGCAGACTTTAGAAATTCTAAAATACATGCAGAAGAAAAAAGAGTCCACCAGTTCAACTGGAGAACAGATTCTTA
CTGGCGGATAACCTGTATTGCAAAGCTTCAGTTCCTCCTACTGATAAAGTGTGTCTGTGGTTGGGGGCTAATGTAATGCT
TGAATATGACATTGATGAAGCTCAGGCATTGTTGGGAAAGAATTTATCAACTGCCAAGAAGAATCTTAAGTCTCTTGAGG
CAGACCTTGACTTTCTTAGAGATTAGTTCACTACCACAGACAGAAGTGAATATGGCCAGGGCTTAGAATAGGGATGTCAA
AAGAAGTAATACAGATGAATCTACCAAGAACAAAGCT

Alignment

ORF - retro_amel_1232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.78 %
• Parental protein coverage: 73.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LDEYHKYKFMELNLAQKKRRLKGQIPEIKQTLEILKYMQKKKKESTSS-LETRFLLADNLYCKASVPPTD
          ...YHKYKFMELNLAQ.KR.LKGQ.PEIKQTLEILKYMQKKK.ESTSS.LE.RFLLADNLYCKASVPPTD
Retrocopy MNSYHKYKFMELNLAQRKRSLKGQNPEIKQTLEILKYMQKKK-ESTSS>LENRFLLADNLYCKASVPPTD

Parental  KVCLWLGANVMLEYDIDEAQALLEKNLSTAMKNLDSLEEDLDFLRDQF-TT-TELDMARVYNWDVKRRNK
          KVCLWLGANVMLEYDIDEAQALL.KNLSTA.KNL.SLE.DLDFLRD.F.TT.TE..MAR..N.DVKR.N.
Retrocopy KVCLWLGANVMLEYDIDEAQALLGKNLSTAKKNLKSLEADLDFLRD*FTTT>TEVNMARA*NRDVKRSNT

Parental  DDSTKNKA
          D.STKNKA
Retrocopy DESTKNKA

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_1232 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1232 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 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009058	2 retrocopies	retro_amel_1232 , retro_amel_1346,
Canis familiaris	ENSCAFG00000019639	2 retrocopies	retro_cfam_1030, retro_cfam_573,
Cavia porcellus	ENSCPOG00000013652	1 retrocopy	retro_cpor_466,
Dasypus novemcinctus	ENSDNOG00000019432	1 retrocopy	retro_dnov_694,
Dipodomys ordii	ENSDORG00000004628	2 retrocopies	retro_dord_213, retro_dord_587,
Latimeria chalumnae	ENSLACG00000016144	1 retrocopy	retro_lcha_18,
Macaca mulatta	ENSMMUG00000015095	1 retrocopy	retro_mmul_124,
Mus musculus	ENSMUSG00000031197	1 retrocopy	retro_mmus_2220,
Nomascus leucogenys	ENSNLEG00000014475	1 retrocopy	retro_nleu_537,
Oryctolagus cuniculus	ENSOCUG00000017448	2 retrocopies	retro_ocun_233, retro_ocun_747,
Otolemur garnettii	ENSOGAG00000016566	1 retrocopy	retro_ogar_3121,
Sarcophilus harrisii	ENSSHAG00000002823	1 retrocopy	retro_shar_7,
Sus scrofa	ENSSSCG00000012811	1 retrocopy	retro_sscr_131,
Ictidomys tridecemlineatus	ENSSTOG00000006684	1 retrocopy	retro_itri_1492,
Tupaia belangeri	ENSTBEG00000007833	5 retrocopies	retro_tbel_3084, retro_tbel_3369, retro_tbel_3652, retro_tbel_553, retro_tbel_632,
Tarsius syrichta	ENSTSYG00000002205	1 retrocopy	retro_tsyr_2032,
Tursiops truncatus	ENSTTRG00000016258	1 retrocopy	retro_ttru_988,