RetrogeneDB ID: retro_amel_540

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192493.1:809241..809636(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT21
• Ensembl ID: ENSAMEG00000016628
• Aliases: None
• Description: None

Sequence

>retro_amel_540
ATGTCCATGGCACCATCCAATCATTCACAAACCAGCTGGCCCCAGGGGGTCAACCATTTTGGCAGTAAGTACATCCAGGA
GACCCAGCCCCTCACCCTGGAGCAAACCATCAACCTGTACGCTTTTACCAATTATACTTTAGGTACAACGAGTCTTTCTA
TGAGAAGGACAGCTCTGCTGCAGCCAGATTTCAGTGCAGGAGGGAGGAATTTGATAAAATTCGAATGAGAAGAACTGCAG
GAGCGGTTCTGAGTGTATATGAGCACTGGCTACCGCATGTGTTACTGGTATAGCTAGGAACACCTTTCTTCAAAATACCT
GGTGGTGAACTTAAGCCAGGAGGAGATGAAGTTGAAGGACTAAAGCGCTTAATGACAAAAGTCATTAAGAAAGAG

Alignment

ORF - retro_amel_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.92 %
• Parental protein coverage: 58.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVVPPNRSQTGWPRGVNQFGNKYIQQTKPLTLERTINLYPLTNYTFGT-KEPLYEKDSSVAARFQRMRE
          MS..P.N.SQT.WP.GVN.FG.KYIQ.T.PLTLE.TINLY..TNYT.GT..E..YEKDSS.AARFQ..RE
Retrocopy MSMAPSNHSQTSWPQGVNHFGSKYIQETQPLTLEQTINLYAFTNYTLGT<NESFYEKDSSAAARFQCRRE

Parental  EFDKIGMRRTVEGVLIVHEHRLPHVLLLQLGTTFFKLPGGELNPGEDEVEGLKRLMTEILGRQ
          EFDKI.MRRT...VL.V.EH.LPHVLL..LGT.FFK.PGGEL.PG.DEVEGLKRLMT......
Retrocopy EFDKIRMRRTAGAVLSVYEHWLPHVLLV*LGTPFFKIPGGELKPGGDEVEGLKRLMTKVIKKE

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_540 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_540 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016628	1 retrocopy	retro_amel_540 ,
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Equus caballus	ENSECAG00000001043	1 retrocopy	retro_ecab_292,
Erinaceus europaeus	ENSEEUG00000003402	1 retrocopy	retro_eeur_35,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Myotis lucifugus	ENSMLUG00000004968	2 retrocopies	retro_mluc_1576, retro_mluc_999,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,
Tupaia belangeri	ENSTBEG00000007664	1 retrocopy	retro_tbel_4003,
Vicugna pacos	ENSVPAG00000003701	2 retrocopies	retro_vpac_340, retro_vpac_605,