RetrogeneDB ID: retro_amel_1861

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194929.1:70824..71321(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS25
• Ensembl ID: ENSAMEG00000004349
• Aliases: None
• Description: mitochondrial ribosomal protein S25 [Source:HGNC Symbol;Acc:14511]

Sequence

>retro_amel_1861
ATGCCCATGAAAGGCTGCTTCTTGATCTGCCACACCTTGCAGTACCTGGGCCGGGGGAGATGGTATTCAAGATCAGTGAA
GGTGATGACTGTGAACTACAACATGCATGAGGAGCTGGGTGAGGGCACCAGGATATTTGTGGTTTTCAATATATCTAAGA
TCCTATACAAAAAGCCTTGGGTGCAGATCATGATGTTTAAGAACATGATGCCATCCCCATTTCTGTGGTTCTATCTGCAT
TCCAGAGAGTAGGTCCTCATGGATGTGGAGACCAAGTATAATAAATAGATCATAAAGCACATCCAATAAATCTTGGGGAA
GAATAAGGAAACCTCAAAAAGAGGAATAGAGAAAAAGCAGGTTTCTCACCCAGCCCACTTTGGCCCCCAAAAGTACTGCC
TGCTGAAGCGCATCTGTTAGGTAAAGGGCAAGTCCCCGGCCTGGGCCTGGTGCCATTACCCAAGGAGATGACAGGGAAAT
ACAAAGCAATGCTGAAG

Alignment

ORF - retro_amel_1861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 97.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLMKGRFSIRRTLQYLGQGDVVFKDSVKVMTVNYNTHGELGEGARKFVFFNIPQIQYKNPWVQIMLFKNM
          M.MKG.F.I..TLQYLG.G......SVKVMTVNYN.H.ELGEG.R.FV.FNI..I.YK.PWVQIM.FKNM
Retrocopy MPMKGCFLICHTLQYLGRGRW-YSRSVKVMTVNYNMHEELGEGTRIFVVFNISKILYKKPWVQIMMFKNM

Parental  TPSPFLRFYLDSGEQVLVDVETRSNKEIMEHIRKILGKNKETLEKEEQEKKELSHPAHFGPRKYCLRECI
          .PSPFL.FYL.S.E.VL.DVET..NK.I..HI..ILGKNKET..K...EKK..SHPAHFGP.KYCL...I
Retrocopy MPSPFLWFYLHSRE*VLMDVETKYNK*IIKHIQ*ILGKNKET-SKRGIEKKQVSHPAHFGPQKYCLLKRI

Parental  CEV-EGQVPCPGLVPLPKELTGKYKAMLK
          C.V..GQVP..GLVPLPKE.TGKYKAMLK
Retrocopy C*V<KGQVPGLGLVPLPKEMTGKYKAMLK

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_1861 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1861 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004349	1 retrocopy	retro_amel_1861 ,
Canis familiaris	ENSCAFG00000028683	1 retrocopy	retro_cfam_2200,
Echinops telfairi	ENSETEG00000008261	2 retrocopies	retro_etel_1144, retro_etel_1227,
Felis catus	ENSFCAG00000027687	1 retrocopy	retro_fcat_2014,
Latimeria chalumnae	ENSLACG00000009006	1 retrocopy	retro_lcha_49,
Loxodonta africana	ENSLAFG00000022178	1 retrocopy	retro_lafr_1068,
Mustela putorius furo	ENSMPUG00000017248	1 retrocopy	retro_mputfur_1608,
Oryctolagus cuniculus	ENSOCUG00000006984	1 retrocopy	retro_ocun_1040,
Ochotona princeps	ENSOPRG00000009370	3 retrocopies	retro_opri_288, retro_opri_690, retro_opri_951,
Pelodiscus sinensis	ENSPSIG00000008882	1 retrocopy	retro_psin_36,
Tursiops truncatus	ENSTTRG00000009881	1 retrocopy	retro_ttru_140,