RetrogeneDB ID: retro_amel_1163

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192980.1:496912..497881(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPA2
• Ensembl ID: ENSAMEG00000013824
• Aliases: None
• Description: non imprinted in Prader-Willi/Angelman syndrome 2 [Source:HGNC Symbol;Acc:17044]

Sequence

>retro_amel_1163
GAAGGCCTTATACAACTTGCCAGGAAGGACTCCATGAAAGCAGGTCAAGGTGGCCATGCACATCTTAAATAATGGTTGAG
GTAGGCTGGATTGCTATCAATGGGAGCAGGTGAGGTGGCCAACTTTGCTGCATATGCCTTTGCACCAGCCACCCTAGTGA
CTCCGTTCGGATGCTCTCAGCATCCAAGTAAGTGCCATTCTTGCTTCATACTTTCTGAATGAAAGACTTAATCTTCATGG
GAAAATTGGATGTTTGCTAAGTATTCTAGGATCTACAGTTATGGTCCTTCATGCTCCAAAAGAAGAGGAGATCGAGACTT
TAAATGAAATGTCTCACAAGCTGGGAGACCCAGGTTTTGTGGTCTTTGCAACACTTGTGTTCATTGTGTCATTGGTATTA
ATCTTCATGGTGGGACCTCACCATGGACAGACCAACAATCTTGTGTACATAACAATCTGCTCTGTAATTGGAACGTTTTC
AGCCTCCTGTGTTAAGGGCTTGGGCGTTGTTATCGAAGGGCCCTTTGCTGGAAAGCCTGTGCTACAACATTCCCTGGCCT
GGATTCTGCTGCTGAGCCTTACAGTCTGTGTGAGCACACAGATTAATTACCTAAACAGGGCCCTGGATGTATTCAACACT
TCCATTGTGACTCCCAAAATATTACGTATTCTTTACAACATCAGTTTTAACTTGTTTAGCTATTCTTTTTAAGGAGTGGC
AAGATATGCCTGTTGATGATGTCACTGGTACTTTGGGTGGCTTCTTTACAATCATGTTGGGAAATTCTTGTTGCATGCCT
TTAAAGATGTCAGCTTTACTCTCCCTGTGTCTTTTCAAAAAGACGAAAAAGCAAGGAATGGCAATCTAACATGTATGAAG
TTCTTAATAATGAAGAAAGCTTAACCTGTGGAATTGAACAACACAGTGGTGAAAATATCTCCTGAAGAAATGGAAATCTC
ACAGCTTTT

Alignment

ORF - retro_amel_1163 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.23 %
• Parental protein coverage: 91.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KGLLRLARKGSMRAGQGGHAYLKEWLWWAGLLSMGAGEVANFAAYAFAPATLVTPLG-ALSVLVSAILSS
          .GL..LARK.SM.AGQGGHA.LK.WL..AGLLSMGAGEVANFAAYAFAPATLVTP.G.ALS..VSAIL.S
Retrocopy EGLIQLARKDSMKAGQGGHAHLK*WLR*AGLLSMGAGEVANFAAYAFAPATLVTPFG>ALSIQVSAILAS

Parental  YFLNERLNLHGKIGCLLSILGSTSMIIHAPKEEEIETLNEMSHKLGDPGFVVFATLVVIVSLILIFVVGP
          YFLNERLNLHGKIGCLLSILGST.M..HAPKEEEIETLNEMSHKLGDPGFVVFATLV.IVSL.LIF.VGP
Retrocopy YFLNERLNLHGKIGCLLSILGSTVMVLHAPKEEEIETLNEMSHKLGDPGFVVFATLVFIVSLVLIFMVGP

Parental  RHGQTNILVYITICSVIGALSVSCVKGLGIAIKELFAGKPVLRHPLAWILLLSLTVCVSTQINYLNRALD
          .HGQTN.LVYITICSVIG..S.SCVKGLG..I...FAGKPVL.H.LAWILLLSLTVCVSTQINYLNRALD
Retrocopy HHGQTNNLVYITICSVIGTFSASCVKGLGVVIEGPFAGKPVLQHSLAWILLLSLTVCVSTQINYLNRALD

Parental  IFSTSIVTPI-YYVFFTTSVLTCLAILFKEWQDMSVNDVIGTLSGFFTII-VGIFLLHAFKDVSFSLASL
          .F.TSIVTP..YYVFFTTSVLTCLAILFKEWQDM.V.DV.GTL.GFFTI..VG.FLLHAFKDVSF....L
Retrocopy VFNTSIVTPK>YYVFFTTSVLTCLAILFKEWQDMPVDDVTGTLGGFFTIM<VGKFLLHAFKDVSFT---L

Parental  PVS-FRKDEKAMNGNLSNMYEVLNNNEESLTCGIEQHSGENISRRNGNLTAF
          PVS.F.K..K......SNMYEVL.NNEESLTCGIEQHSGENIS.RNGNLTAF
Retrocopy PVS<FSKRRKSKEWQ-SNMYEVL-NNEESLTCGIEQHSGENIS*RNGNLTAF

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_1163 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1163 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013824	1 retrocopy	retro_amel_1163 ,
Choloepus hoffmanni	ENSCHOG00000005553	1 retrocopy	retro_chof_9,
Callithrix jacchus	ENSCJAG00000005448	1 retrocopy	retro_cjac_1506,
Equus caballus	ENSECAG00000006379	1 retrocopy	retro_ecab_656,
Felis catus	ENSFCAG00000023073	1 retrocopy	retro_fcat_246,
Macaca mulatta	ENSMMUG00000003892	1 retrocopy	retro_mmul_1510,
Mus musculus	ENSMUSG00000030452	1 retrocopy	retro_mmus_3551,
Oryctolagus cuniculus	ENSOCUG00000010746	3 retrocopies	retro_ocun_1581, retro_ocun_773, retro_ocun_809,
Ictidomys tridecemlineatus	ENSSTOG00000004003	3 retrocopies	retro_itri_1847, retro_itri_347, retro_itri_388,
Vicugna pacos	ENSVPAG00000000671	1 retrocopy	retro_vpac_285,