RetrogeneDB ID: retro_amel_1330

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193203.1:263440..263967(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LZIC
• Ensembl ID: ENSAMEG00000004171
• Aliases: None
• Description: leucine zipper and CTNNBIP1 domain containing [Source:HGNC Symbol;Acc:17497]

Sequence

>retro_amel_1330
AAAATGCCTTCCAAAGGAAAGACAGAGACAAGCAAATTAAAGCGGAATTTAGAACAGTTGGATAGACTAATGCAGCAATT
ACAGGACTTGGAGGAATCCAGAGAGGGACTTGTTACAGATGACTATGAAGAAACCAAAAAGGAAACTCTGGAGCAACTAA
GTGAATTTAATGATTCACTGAAAAAACTATGCCTGGAAATATGACTTTGGTAGATGAGCTAAGTTGAGTGCAACTAGCTA
ACCAGGCAGCTATCAGCCAGGCCTTTCAAACCCTGGAGGTGATCAGATTACCTGCAAAGAAACAACCAGGTCAGCTTCGG
ACAAGGTTAGCAGAGATGGATAGAGATCTCATGGTGGGAAAGCTGGAAAGAGGCCTCTATACTCAACAGAAAGTGTAGAT
ACTAACAGCTCTCAGGACACTTGGAGAGAAGCTGACTGCGGATGACGAGGCCTTCTTGTCAGCAAATGCAGGTGCTCTAC
TCAGCCAGTTTGAGAAAGTCTCTACAGACCTTGGCTCTGGAGACAAG

Alignment

ORF - retro_amel_1330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.76 %
• Parental protein coverage: 83.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMASRGKTETSKLKQNLEEQLDRLMQQLQDLEECREELDTDEYEETKKETLEQLSEFNDSLKKI-MSGNM
          KM.S.GKTETSKLK.NLE.QLDRLMQQLQDLEE.RE.L.TD.YEETKKETLEQLSEFNDSLKK..M.GNM
Retrocopy KMPSKGKTETSKLKRNLE-QLDRLMQQLQDLEESREGLVTDDYEETKKETLEQLSEFNDSLKKL<MPGNM

Parental  TLVDELSGMQLAIQAAISQAFKTPEVIRLFAKKQPGQLRTRLAEMDRDLMVGKLDRGLYTQQKVEILTAL
          TLVDELS..QLA.QAAISQAF.T.EVIRL.AKKQPGQLRTRLAEMDRDLMVGKL.RGLYTQQKV.ILTAL
Retrocopy TLVDELS*VQLANQAAISQAFQTLEVIRLPAKKQPGQLRTRLAEMDRDLMVGKLERGLYTQQKV*ILTAL

Parental  RKLGEKLTADDEAFLSANAGALLSQFEKVSTDLGSGDK
          R.LGEKLTADDEAFLSANAGALLSQFEKVSTDLGSGDK
Retrocopy RTLGEKLTADDEAFLSANAGALLSQFEKVSTDLGSGDK

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_1330 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1330 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004171	2 retrocopies	retro_amel_1330 , retro_amel_1820,
Echinops telfairi	ENSETEG00000011633	1 retrocopy	retro_etel_686,
Felis catus	ENSFCAG00000023559	1 retrocopy	retro_fcat_1666,
Mustela putorius furo	ENSMPUG00000016545	2 retrocopies	retro_mputfur_336, retro_mputfur_524,