RetrogeneDB ID: retro_amel_1002

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192812.1:486207..486805(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIT2
• Ensembl ID: ENSAMEG00000003980
• Aliases: None
• Description: nitrilase family, member 2 [Source:HGNC Symbol;Acc:29878]

Sequence

>retro_amel_1002
TGGGAGAGCCATGCCACTTTCCATTTGGTCCTCATCCAACTTCAGGTTTCTTCCATCAAATCAGATAACCTCTCTCAAGC
TTGTGGCCTTGTCCGGGAGGCTGCAACAGAAGGAGTCAAAATAGTTTCTCTACCAGAATGCTTTAATTCTCCATTTGGCA
TGAAATATTTTCCTGAACATGCAGAGAAAATTCCAGGTGAAGCCACACAGGAGCTTTCTGAAGTAGCAAAGGAGTGCAGC
ATATATCTCATTGGAGGTTCCATTCTTGAAGAGGATGCTGGGAGATTATATAACACCTGTGCCATATTAGGCCTGATGGA
ATTTTACTGGTAGAGCATAGAAAGCACCATCTGTTTGACATTGATGTTCCTGGGAAAATTACATTTCAAGAGTCTAAAGC
ATTGAGTCCTGGTGATAGTTTTTCCACATTTGATAATCCTTATTGCAGAGTGGGCTTGGGCATCTGCTATGACATTGCTT
TGTGGAGCTTGCACAAATCTACATACAGAGGGCCTGGCAGCTGTTGGTATATCCCAGAGCTTTTAATTTGACTTCTGGAC
CAGTCCACTGGGAGTTGCTTCAGTGAGGCCAGGCTGTT

Alignment

ORF - retro_amel_1002 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.45 %
• Parental protein coverage: 71.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FSSSSAFRLALIQLQVSSIKSDNLARACSLVREAATRGAKIVSLPECFNSPYGTKYFPEYAEKIPGESTE
          ..S...F.L.LIQLQVSSIKSDNL..AC.LVREAAT.G.KIVSLPECFNSP.G.KYFPE.AEKIPGE.T.
Retrocopy WESHATFHLVLIQLQVSSIKSDNLSQACGLVREAATEGVKIVSLPECFNSPFGMKYFPEHAEKIPGEATQ

Parental  KLSEVAKECGIYLIGVKGSIPEEDAGKLYNTCTVFG-PDGTLLVKYRKLHLFDIDVPGKITFQESKILSP
          .LSEVAKEC.IYLIG..GSI.EEDAG.LYNTC...G.PDG.LLV..RK.HLFDIDVPGKITFQESK.LSP
Retrocopy ELSEVAKECSIYLIG--GSILEEDAGRLYNTCAILG<PDGILLVEHRKHHLFDIDVPGKITFQESKALSP

Parental  GDSFSTFDTPYCRVGLGICYDMR-FAELAQIYAQRGCQLLVYPGAFNMTTGPAHWELLQRGRAV
          GDSFSTFD.PYCRVGLGICYD...F.ELAQIY.QR..QLLVYP.AFN.T.GP.HWELLQ.G.AV
Retrocopy GDSFSTFDNPYCRVGLGICYDIA<FVELAQIYIQRAWQLLVYPRAFNLTSGPVHWELLQ*GQAV

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_1002 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1002 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003980	1 retrocopy	retro_amel_1002 ,
Callithrix jacchus	ENSCJAG00000000590	1 retrocopy	retro_cjac_3014,
Homo sapiens	ENSG00000114021	1 retrocopy	retro_hsap_411,
Gorilla gorilla	ENSGGOG00000003724	1 retrocopy	retro_ggor_406,
Macaca mulatta	ENSMMUG00000020024	2 retrocopies	retro_mmul_1758, retro_mmul_505,
Mustela putorius furo	ENSMPUG00000011450	1 retrocopy	retro_mputfur_805,
Nomascus leucogenys	ENSNLEG00000002631	1 retrocopy	retro_nleu_1009,
Pan troglodytes	ENSPTRG00000015161	1 retrocopy	retro_ptro_315,