RetrogeneDB ID: retro_amel_1592

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193683.1:361211..361636(-)
• Located in intron of: ENSAMEG00000000949

Retrocopy information

• Ensembl ID: ENSAMEG00000000970
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FIGLA
• Ensembl ID: ENSAMEG00000015931
• Aliases: None
• Description: folliculogenesis specific basic helix-loop-helix [Source:HGNC Symbol;Acc:24669]

Sequence

>retro_amel_1592
CTCCAATTGGTGCTGGAGCAGGGTGCGTGGCCAACAGCAAGGAGCACGAGCAGATAAAAAAATCTCAACCTTGGTTTTGC
CAAACTGAAGAGACTTGTGCCACTTCTTCCCCGAAGCAGGAAACCTACCAAGCTGATATCCTTCAAGGTGCAAATGAACA
CATACAGGTTCTCAGTGATGTTTTCAGAGAAGCCAGAGACTCAGACACAAAATCCAGATCACCAAACTACAACAATACTT
CTGAACCACACATACCCTTGGCTGGAAACCTATCAAGAAACATCGCCCAGCATGCCAGCTGTACTGTGGGCTTGAAGAAT
GAGGAGGAAAGGCCCGGGGCCGATGGTGGCAGTGGTGAGTCAGCACACACTTGTCACCAGTGCGTGATGTCTACGACTGG
AGTTATCTCCCCAACCAAGAGTCTG

Alignment

ORF - retro_amel_1592 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.75 %
• Parental protein coverage: 65.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LQLVLERRR-VANAKERERI-KNLNRGFAKLKALVPFLPQSRKPSKV-DILKGATEYIQVLSDVLEGAKD
          LQLVLE....VAN.KE.E.I.KNLN.GFAKLK.LVP.LP.SRKP.K..DIL.GA.E.IQVLSDV...A.D
Retrocopy LQLVLEQGA<VANSKEHEQI>KNLNLGFAKLKRLVPLLPRSRKPTKL<DILQGANEHIQVLSDVFREARD

Parental  SERQNPDHQNYRNNPSEPPISLARDLSRNITQHASCTVGLKNEEERPWADGGSGESAYTCRQSVMSTTGV
          S........NY.NN.SEP.I.LA..LSRNI.QHASCTVGLKNEEERP.ADGGSGESA.TC.Q.VMSTTGV
Retrocopy SDTKSRS-PNY-NNTSEPHIPLAGNLSRNIAQHASCTVGLKNEEERPGADGGSGESAHTCHQCVMSTTGV

Parental  ISPARSL
          ISP..SL
Retrocopy ISPTKSL

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_1592 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1592 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015931	1 retrocopy	retro_amel_1592 ,
Callithrix jacchus	ENSCJAG00000019358	1 retrocopy	retro_cjac_3644,
Felis catus	ENSFCAG00000013444	1 retrocopy	retro_fcat_159,