RetrogeneDB ID: retro_amel_120

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192610.1:1391341..1391737(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000019842
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CCDC169
• Ensembl ID: ENSAMEG00000004615
• Aliases: None
• Description: None

Sequence

>retro_amel_120
ATGGAAAAAATCCGTGGAAATCCTTCAGATAGACTCGCTTCTATTCGTGTCTATGAGCGAATGCCAGTGGAATCCTTAAA
TACATTACTTAAACAGCTAGAAAAGGAAAAGAGGAGTCTTGAAAATCAAGTGAAAAACTGTGCACTTAGACTGGAACAAG
AGTCAAAGGCTTACCATAAGACCAATGATGAACGCCGCGTCTACCTGGCTGAAATGTCTCTGATCTCTGGCTCACACCAA
GTTTCTAAAAGGCAACAGATGGATCAACTTCATAGAATTAAAGAGAATCATGTGAAAGCAGGAAGACATGATCCTGCTAA
TCAGAAGATAGTGAATGCCAAGAAAGGGCCAGCAAAAAAGATTACAAAACCAAACCATCTGCCAAAACTCAATCCA

Alignment

ORF - retro_amel_120 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.79 %
• Parental protein coverage: 81.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEKIRGNPLDRLSSIFVYEQMPVEYLNTLLKQLEKEKRSLENQVKNCALRREQESKAYHKTTNECCRYLA
          MEKIRGNP.DRL.SI.VYE.MPVE.LNTLLKQLEKEKRSLENQVKNCALR.EQESKAYHKT..E...YLA
Retrocopy MEKIRGNPSDRLASIRVYERMPVESLNTLLKQLEKEKRSLENQVKNCALRLEQESKAYHKTNDERRVYLA

Parental  EMSRVSDSYQVSKRQQMDQLPRMKENLVKMGRYNPVNQKTMNAKRGPVKKITRSNHLPKLNP
          EMS..S.S.QVSKRQQMDQL.R.KEN.VK.GR..P.NQK..NAK.GP.KKIT..NHLPKLNP
Retrocopy EMSLISGSHQVSKRQQMDQLHRIKENHVKAGRHDPANQKIVNAKKGPAKKITKPNHLPKLNP

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_120 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_120 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004615	1 retrocopy	retro_amel_120 ,
Equus caballus	ENSECAG00000011446	1 retrocopy	retro_ecab_111,
Felis catus	ENSFCAG00000008786	1 retrocopy	retro_fcat_39,
Oryctolagus cuniculus	ENSOCUG00000026427	1 retrocopy	retro_ocun_406,
Otolemur garnettii	ENSOGAG00000010367	2 retrocopies	retro_ogar_1996, retro_ogar_957,
Sus scrofa	ENSSSCG00000026564	1 retrocopy	retro_sscr_77,