RetrogeneDB ID: retro_amel_915

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192741.1:1479855..1480455(-)
• Located in intron of: ENSAMEG00000010821

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000013028
• Aliases: None
• Description: Regucalcin [Source:UniProtKB/TrEMBL;Acc:G1M307]

Sequence

>retro_amel_915
GTGGAGTAAGTGACCACAGTTGCCCCCATCAACTCTGTGACACTTCACCTGGCAGGCTATGTCACCACCATTAGAACAAA
GTTCTGTGCTTAAACTGAGAAGATCAGTCAACAGTTGTCCTGGCCACAGTAGATAAAGACAAGAAAAACAATCAGTTCAA
TAATGGGAAGGTGGATGCCACTGGGAGATACTTTGCTGACAGTATGGCTGAGGAAACGGCCCCACCAGTACTGAAGCGGC
ACCAGAGGTCCCTGTACTCTCTTTTCCTGACCATGATGTGGAAAAGACTTTGGCCAGGTACACATCTACAATGGTTTGGA
TTGGCCCCTAAACCACAAAATCTTCTATTACATTGACAGTCTGTCCTATTCTGTAGATGCTTTTGATTATGACATGCAAA
CAGGAAAGATCTCCAACTGCAGAAGTGTTTACAAGCTGGAGAAAGAAGAATAAATTCCAGATAGAATGTGTATTGATGCT
GAGGGGGAGCTCTGGGTGGCCTGTTACAATGGAGGAAGAGTGATTCTTTTAGATCCTAAGACAAGGAAAAGACTCCAGAC
TGTGAAGTTGCCTGTTGATAAAACAACTTCATGCTGCTTC

Alignment

ORF - retro_amel_915 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.56 %
• Parental protein coverage: 67.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VQQVTVEAPVSSVALRQGGGYVATIGTKFCA-LNWEDRSAVALATVDKDKKNNRFNDGKVDPAGRYFAGT
          V..VT..AP..SV.L...G.YV.TI.TKFCA.LN.ED.S.V.LATVDKDKKNN.FN.GKVD..GRYFA..
Retrocopy VE*VTTVAPINSVTLHLAG-YVTTIRTKFCA<LN*EDQSTVVLATVDKDKKNNQFNNGKVDATGRYFADS

Parental  MAEETAPAVLERHQGSLYSLF-PDHHVEKY-FDQVDISNGLDWSLDHKIFYYIDSLSYSVDAFDYDLQTG
          MAEETAP.VL.RHQ.SLYSLF.PDH.VEK..F.QV.I.NGLDW.L.HKIFYYIDSLSYSVDAFDYD.QTG
Retrocopy MAEETAPPVLKRHQRSLYSLF<PDHDVEKT<FGQVHIYNGLDWPLNHKIFYYIDSLSYSVDAFDYDMQTG

Parental  KISNRRSVYKLEKEEQIPDGMCIDTEGKLWVACYNGGRVIRLDPETGKRLQTVKLPVVKTTSCCF
          KISN.RSVYKLEKEE.IPD.MCID.EG.LWVACYNGGRVI.LDP.T.KRLQTVKLPV.KTTSCCF
Retrocopy KISNCRSVYKLEKEE*IPDRMCIDAEGELWVACYNGGRVILLDPKTRKRLQTVKLPVDKTTSCCF

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_915 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_915 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013028	1 retrocopy	retro_amel_915 ,
Canis familiaris	ENSCAFG00000014821	1 retrocopy	retro_cfam_685,
Monodelphis domestica	ENSMODG00000000375	1 retrocopy	retro_mdom_1797,
Mustela putorius furo	ENSMPUG00000013105	1 retrocopy	retro_mputfur_1618,