RetrogeneDB ID: retro_amel_1655

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193869.1:317199..317688(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000002637
• Aliases: None
• Description: None

Sequence

>retro_amel_1655
AGGCTCTCTAGCCAGCACCTTAGGCACTACTCCCTTGTGCTGTTGGCCTTCACATCATTTCAGCAGGAACTTGATGCAAA
ACATGACAAATATGAGAGACTTAGCCAAGATATAACTGCTGAAAGTAAAAGACAATTTTTCTCCTCCATAGGATTACAAG
TGCTCCTGATATGGAAGATACATTGACAGAATCAGAATTTGAATTGGATGGGAGTAGACAAAAGATATCACAAGTAGCCC
AAGTGCTCTTCAGGAGATGACATGCATCAATTCCATAGAGCCATTACTACAGGGCTGCAGGAATATGTGGAGGCTGTCTC
TTTTCAGCAGTTCATCAGAACATGATCACTTACCAGTATGGATGAAATTAAACAATTGATATTTACAGCAGTAGAATATA
AAAAGAAAATAAGACACCCTCAGCCCTCTGATGCACAGAGGAAGCTGTTTGGAACTGGGAGACTAAAAATCACACCTGTT
GATTACCTT

Alignment

ORF - retro_amel_1655 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.18 %
• Parental protein coverage: 57.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RREGKDVNSSSPVMLAFKSFQQELDARHDKYERLVKLSRDITVESKR-TIFLLHRITSAPDMEEILTESE
          R.........S.V.LAF.SFQQELDA.HDKYER...LS.DIT.ESKR.TIFLLHRITSAPDME..LTESE
Retrocopy RLSSQHLRHYSLVLLAFTSFQQELDAKHDKYER---LSQDITAESKR<TIFLLHRITSAPDMEDTLTESE

Parental  IKLDGVRQKILQVAQEL-SGEDMHQFHRAITTGLQEYVEAVSFQHFIKTRSLISMDEINKQLIFTTEEYG
          ..LDG.RQKI.QVAQ.L.SG.DMHQFHRAITTGLQEYVEAVSFQ.FI.T.SL.SMDEI.KQLIFT..EY.
Retrocopy FELDGSRQKISQVAQVL>SGDDMHQFHRAITTGLQEYVEAVSFQQFIRT*SLTSMDEI-KQLIFTAVEYK

Parental  -KENKTPSS-DAQDKQFGTWRLK-ITPVDYL
          .KENKTPS...........W..K.ITPVDYL
Retrocopy <KENKTPSAL*CTEEAVWNWETK>ITPVDYL

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_1655 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1655 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002637	1 retrocopy	retro_amel_1655 ,
Dasypus novemcinctus	ENSDNOG00000006963	1 retrocopy	retro_dnov_1829,
Felis catus	ENSFCAG00000028088	1 retrocopy	retro_fcat_1789,
Myotis lucifugus	ENSMLUG00000015591	1 retrocopy	retro_mluc_1131,
Mus musculus	ENSMUSG00000056820	1 retrocopy	retro_mmus_393,
Otolemur garnettii	ENSOGAG00000005575	1 retrocopy	retro_ogar_91,
Ictidomys tridecemlineatus	ENSSTOG00000024989	1 retrocopy	retro_itri_259,