RetrogeneDB ID: retro_amel_1917

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL196160.1:1595..2075(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000007079
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KRTAP4-1
• Ensembl ID: ENSAMEG00000008415
• Aliases: None
• Description: None

Sequence

>retro_amel_1917
TGCCAGCCTACGTGCTGCAGGACCACTTGCTGCAGGACCACCTGCTGCCAGCCCAGCTGCTGCGGGTGCAGTGGTGGCTG
TGGACAAGGCGGCTGCGGGTCCAGCTGCTGCGGGTCCAGCTGCTGCCAGCCTTGCTGCTGCCGCCCAACTTGCTGTCAGA
CCACCTGCTGCAGGACCACCTGCTGCCGGCCCAGCTGCTGTGTGTCCAGCTGCTGCCAGCCCAGCTGCTGTGGGTCCAGT
GGCTGTGGACAAACTTGCTGTGGGTCCAGCTGCTGTCAGCCAGCCTGCTGTACCCCTGTGTACTGCAGGAGAACGTGCTA
CCAGCCCACCTGCTGCTGCGTGCCTGGATGCCTAGCCCAGGGCTGTGGATCCAGCTGCTGCTAGCCCGGTTGCCAGCCAA
ACTGCTGCCGCACCACCTGCTGCAGGACCACCTGCTGCCACCCCTGCCGTGTGTCCAGCTGCTGCCAGCCTTCCGACTGC

Alignment

ORF - retro_amel_1917 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.68 %
• Parental protein coverage: 67.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CLPTCCQTTCCRTTCCRPSCCVSS--CCRPSCGSSCCRPSCCISSCCRPTCCQTTCCRTTCCRPSCCVSS
          C.PTCC.TTCCRTTCC.PSCC..S..C....CGSSCC..SCC...CCRPTCCQTTCCRTTCCRPSCCVSS
Retrocopy CQPTCCRTTCCRTTCCQPSCCGCSGGCGQGGCGSSCCGSSCCQPCCCRPTCCQTTCCRTTCCRPSCCVSS

Parental  CCRPSCC-TTCCCPTCCGSSCCRPSCCISSCCRPTC--PSCCVSSCCRPSCGGSSCWGSSCCRPSCCISS
          CC.PSCC....C..TCCGSSCC.P.CC....CR.TC..P.CC....C.P.C....C.GSSCC.P..C...
Retrocopy CCQPSCCGSSGCGQTCCGSSCCQPACCTPVYCRRTCYQPTCC----CVPGCLAQGC-GSSCC*PG-CQPN

Parental  CCRPSCSGSSCCGSSCCQPSCCCPSCC
          CCR..C....CC...C...SCC.PS.C
Retrocopy CCRTTCCRTTCC-HPCRVSSCCQPSDC

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_1917 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1917 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008415	1 retrocopy	retro_amel_1917 ,
Otolemur garnettii	ENSOGAG00000034456	1 retrocopy	retro_ogar_2681,
Pongo abelii	ENSPPYG00000011492	3 retrocopies	retro_pabe_14, retro_pabe_15, retro_pabe_16,
Rattus norvegicus	ENSRNOG00000001218	2 retrocopies	retro_rnor_380, retro_rnor_382,