RetrogeneDB ID: retro_amel_1024

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192837.1:261180..261527(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDTL
• Ensembl ID: ENSAMEG00000013811
• Aliases: None
• Description: None

Sequence

>retro_amel_1024
CCATTCTTCGCGCTGGACACCCACTTGGCTGCCGGCCGCGTGCCCACGGGACTGGAGAAGCGGCTCGGCCCTGCCAGGGC
AGCCATCCTGGGCAAACCTGAGGACCGTGTGGACAGGATGGTGCCACCGGGTCTGGCCCTGGCGGCGAATGGCTCCACGG
TGCCCAGCGCCACCTGCTCATCTCCCCCATCCGTGTGCGGGCACCGCAGAGGAGGACTGCGGCCATGCACGCGAGTCTTC
GGGGTCCTCACAAGGAGCTGGACGCGCGCCAGGATCCGATCATTACGCGCATTCCCCCCCTGGAGATCTAGTAGATTGGC
AAGAAAGGGACAGTCATGAATTTTCTC

Alignment

ORF - retro_amel_1024 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.81 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PFVELDTNLPAGRVPAGLEKRLCAATAAILSKPEDRVNVTVRPGLAMAMNGTTEPCA-QLLISSIAV-VG
          PF..LDT.L.AGRVP.GLEKRL..A.AAIL.KPEDRV...V.PGLA.A.NG.T.P.A..LLIS.I.V..G
Retrocopy PFFALDTHLAAGRVPTGLEKRLGPARAAILGKPEDRVDRMVPPGLALAANGSTVPSA<HLLISPIRV<AG

Parental  TA-ENRGHS-ARFFEFLT-KELNLGQDRIIIRFFPLEPWQIGKKGTVMTFL
          TA.E..GH...R.F..LT.KEL...QD.II.R..PLE...IGKKGTVM.FL
Retrocopy TAEEDCGHA<TRVFGVLT<KELDARQDPIITRIPPLEI**IGKKGTVMNFL

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_1024 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1024 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013811	1 retrocopy	retro_amel_1024 ,
Callithrix jacchus	ENSCJAG00000009483	1 retrocopy	retro_cjac_2434,
Felis catus	ENSFCAG00000009408	1 retrocopy	retro_fcat_1172,
Macaca mulatta	ENSMMUG00000004552	1 retrocopy	retro_mmul_312,
Mustela putorius furo	ENSMPUG00000002935	1 retrocopy	retro_mputfur_1365,