RetrogeneDB ID: retro_amel_68

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192351.1:3703440..3704013(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000019824
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000008614
• Aliases: None
• Description: None

Sequence

>retro_amel_68
ATGGCTCCAGCGTGGGTCCTGGTGCTGGTGACCGTGGTGCTGGGCTTGGCCCGAGCGGGCCCTGTCCCTACTTCCAAACC
CACCACAACCAGGAGGGGCTGCCACATGGACAGGTTCCTGTCTCTGTCACCGAGGGAGCTAGAAGCCTTCAAGAAGGCCA
AGGATGCCTTAGAAGAGTCACTCTCACTGAAGAACTGGAGCTGCAGCTCTCGCCTCTTCCCTAAGGCCTGGGACCTGAGA
CTACTGCAGGCCTGGGAGCGCCCCGTAGCCTTGGAGGCTGAGCTGGACTTGACGCTGAAGGTCCTGGGCGACATGGCTGA
CTCGTCCCTGGGGGCCGTCCTGGACCAGCCCCTCCGCATGCTGCGCCACATCCAAGCCGAGCTCCAGGCTTGCGCCCTGG
CTCAGCCCACAGCAGGACCCAGACCCCGTGGCCGCCTCCACCACTGGCTGCACCGGCTCCAGAAGGCCCCAAAGGAGTCC
CAGGGCTGCCTCGAGGCCTCCATCACCTTCAACCTCTTCCGCCTCCTCACCCAGGACCTGAAATGTGTCGCCAGTGGAGA
CCTGTGCGTCTGA

Alignment

ORF - retro_amel_68 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.01 %
• Parental protein coverage: 96.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMAWVLVLVTAGLSLARAGPVPTSKPTTTWKGCDIGRFKSLSPRELEAFRKAKDALEN--SLKNWSCSS
          MA.AWVLVLVT..L.LARAGPVPTSKPTTT..GC...RF.SLSPRELEAF.KAKDALE...SLKNWSCSS
Retrocopy MAPAWVLVLVTVVLGLARAGPVPTSKPTTTRRGCHMDRFLSLSPRELEAFKKAKDALEESLSLKNWSCSS

Parental  RLFPRNRDLRQLQVWERPVALEAELILTLKVLETMADRSQGGILDQPLHTLRHIHSELQACVEAQPTAGP
          RLFP...DLR.LQ.WERPVALEAEL.LTLKVL..MAD.S.G..LDQPL..LRHI..ELQAC..AQPTAGP
Retrocopy RLFPKAWDLRLLQAWERPVALEAELDLTLKVLGDMADSSLGAVLDQPLRMLRHIQAELQACALAQPTAGP

Parental  QPRGRLHHWLHRLSEASKKESQGCLEASVLFNLFRLLKKDLECVASGDLCV
          .PRGRLHHWLHRL..A..KESQGCLEAS..FNLFRLL..DL.CVASGDLCV
Retrocopy RPRGRLHHWLHRLQKA-PKESQGCLEASITFNLFRLLTQDLKCVASGDLCV

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_68 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_68 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008614	1 retrocopy	retro_amel_68 ,
Canis familiaris	ENSCAFG00000005582	1 retrocopy	retro_cfam_58,
Equus caballus	ENSECAG00000005085	1 retrocopy	retro_ecab_56,
Felis catus	ENSFCAG00000010737	1 retrocopy	retro_fcat_111,
Monodelphis domestica	ENSMODG00000023790	1 retrocopy	retro_mdom_1793,
Mustela putorius furo	ENSMPUG00000017733	1 retrocopy	retro_mputfur_164,