RetrogeneDB ID: retro_amel_1192

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193023.1:314875..315343(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FOLR4
• Ensembl ID: ENSAMEG00000011928
• Aliases: None
• Description: folate receptor 4, delta (putative) [Source:HGNC Symbol;Acc:32565]

Sequence

>retro_amel_1192
ACAAACTGGAAAACCCACCTGGATGAGTTCCTGCTATACAACTTCAGTTTGGTTCACTGCAGAATGATGACCCTGGGGCT
GTCAGAAGCACTTCATCCAGGCCGTCTGCTTCTATGAGTGCTCCTTGAACCTGCGACCTTGGAGCCAGCTGGTGGACCCC
ACTGGGCAGGGAGAGCCAACATCTGGCATGACACTATGCTGGGAAAATTGTGAACGGTAGTGGGCAAAATGCCGCACAGT
TTACACTTGCAGAGCCAACTGGCTGGCAGCTGGGACTGGAGTTGGGGGGAAGAACCACTTCCCTGCCAGGGCCTTCTGCC
CCCCCCCCTTTCTCTTTTACTGCCGCTCCCTGCTGACCTGTGTGAGAAGATTGGGAGCAACTCCTTGGAGGCGAACCCCA
GGTACCGGAACAGTGGGCAGTATCTGCAGAAGTGGTTCAGGCCTGCTTAGAGGCACCCAAATGTGGCC

Alignment

ORF - retro_amel_1192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.53 %
• Parental protein coverage: 60.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TSWEAHLDASLLYTFSLLHCGVMMPG-CEKHFLQAICFYECSPNLGPWIQKMDSSGPGERILDAPLCQED
          T.W..HLD..LLY.FSL.HC..M..G.C.KHF.QA.CFYECS.NL.PW.Q..D..G.GE......LC.E.
Retrocopy TNWKTHLDEFLLYNFSLVHCRMMTLG>CQKHFIQAVCFYECSLNLRPWSQLVDPTGQGEPTSGMTLCWEN

Parental  CEQWWEDCRTSYTCKSNW-HGDWNRSGGKNRCPARAICHPFPHYF-PTPADLCEKIWNHSFKASPEPRNS
          CE..W..CRT.YTC..NW..G.W..S.G....P.............P.PADLCEKI...S..A.P..RNS
Retrocopy CER*WAKCRTVYTCRANW<AGSWDWSWGEEPLPCQGLLXXXXSLLLPLPADLCEKIGSNSLEANPRYRNS

Parental  GQCLQKWFEPAQGNPNVA
          GQ.LQKWF.PA...PNVA
Retrocopy GQYLQKWFRPA*RHPNVA

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_1192 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1192 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011928	2 retrocopies	retro_amel_1133, retro_amel_1192 ,
Equus caballus	ENSECAG00000007254	1 retrocopy	retro_ecab_415,
Loxodonta africana	ENSLAFG00000032394	1 retrocopy	retro_lafr_913,
Sus scrofa	ENSSSCG00000014952	1 retrocopy	retro_sscr_282,