RetrogeneDB ID: retro_amel_423

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192436.1:1077809..1078674(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHAX
• Ensembl ID: ENSAMEG00000010042
• Aliases: None
• Description: phosphorylated adaptor for RNA export [Source:HGNC Symbol;Acc:10241]

Sequence

>retro_amel_423
GAGGAGGTTAACGACATAGGGGGCGCTGGGCTACAAGAACGGAGTCAAGGCACAGTGGCCGCTGAACTTGGTGTCTTGGG
AATGGAGGGTGCTATTGACAGAAGCAGACAACGGGAGACCTGCAATGATTTGCTTGCTTAGAAACTTAGGAGGAAATTTC
AAGAACACACAAAAAAATTAGACAAAGACCTAGATGACGATATGCACGGTGGCCAAAAAGATGGGATCAAAGGAAAATGG
GCAAGGTGGTCTCACACAGAACTGACCTGCTAAAGACAGGCAAGGGGACAGACTAGGAATGAACTCTAAAGGCCGGTATC
AGATCACAGAGGACGATTCACAGGAGAAACGGGCTGATGATATTTCTTTCAGTTTGCGGGAAATTTCTTTCAGATTGCAG
ATCTTTCCAGAGAAAGATCTGGTAGCACAAGTAGTGAGGATAATGGGGAACAAAACGGTAACTGACCTTCTGATGAAAAC
TGCCAAAGTTGAACAAACTGCTGGCCTTTTCATAATGAATGCTAGTCAAAGAAAAACACCAGGTGGAGTTTTCCTGGATC
TCCTGAAAAGCACTCCCAGCGTCAGCGAGGAATAAGCGAAGGACATTTTCTACATTGAAAATCAAAAGCAGTATGAACAT
AAAAAAGCTGCTAGGAAGAGAACACAAGTGTTGGGGAAAAAAGATGAAACAAGCTATTAAAAATCTAAATGTTCAAGAAG
ATGGAGACGCATCATGAGAAACTTTGCAAGTGACACCAATGAGGCACTGGCCTCTCTTGCCGAGCCCCCGGAAAGCCACA
CAGAGGCCACGGTGGATGCATAGGAAGTCACTGAGGTTGATCGTTCTCATGATGTGGACATCTTT

Alignment

ORF - retro_amel_423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.27 %
• Parental protein coverage: 70.57 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKVNNIWGAVLQEQNQDAVATELGILGMEGTIDKSRQSETYNYLLAKKLKRESQEHTKELDKELDEYMHG
          ..VN.I.GA.LQE..Q..VA.ELG.LGMEG.ID.SRQ.ET.N.LLA.KL.R..QEHTK.LDK.LD..MHG
Retrocopy EEVNDIGGAGLQERSQGTVAAELGVLGMEGAIDRSRQRETCNDLLA*KLRRKFQEHTKKLDKDLDDDMHG

Parental  -SKKMGSKEEENGQGHLKRKRPVK----DRLGDRLEMNYKGRYEITEDDSQEKVA---DEISFRLQE-PK
          ..KKMGSKE..NGQG.L....P.K....DRLG......Y....................EISFRLQ..P.
Retrocopy >AKKMGSKE--NGQGGLTQN*PAKDRQGDRLGMNSKGRYQITEDDSQEKRADDISFSLREISFRLQIFPE

Parental  KDLIARVVRIIGNKKAIELLMETAEVEQNGGLFIMNGSRRRTPGGVFLNLLKNTPSISEEQIKDIFYVEN
          KDL.A.VVRI.GNK....LLM.TA.VEQ..GLFIMN.S.R.TPGGVFL.LLK.TPS.SEE..KDIFY.EN
Retrocopy KDLVAQVVRIMGNKTVTDLLMKTAKVEQTAGLFIMNASQRKTPGGVFLDLLKSTPSVSEE*AKDIFYIEN

Parental  QKEYENKKAARKRRTQVL-GKKMKQAIKNLNFQEDDDTSRET-FASDTNEALASLDEPQEGHGETKLDAE
          QK.YE.KKAARK.RTQVL.GKKMKQAIKNLN.QED.D.S.ET.FASDTNEALASL.EP.E.H.E...DA.
Retrocopy QKQYEHKKAARK-RTQVL>GKKMKQAIKNLNVQEDGDAS*ET<FASDTNEALASLAEPPESHTEATVDA*

Parental  EAIEVDHSHDLDIF
          E..EVD.SHD.DIF
Retrocopy EVTEVDRSHDVDIF

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_423 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_423 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010042	1 retrocopy	retro_amel_423 ,
Canis familiaris	ENSCAFG00000000590	2 retrocopies	retro_cfam_1136, retro_cfam_1701,
Myotis lucifugus	ENSMLUG00000000184	1 retrocopy	retro_mluc_1483,