RetrogeneDB ID: retro_amel_673

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192563.1:1282072..1282660(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RDH12
• Ensembl ID: ENSAMEG00000008036
• Aliases: None
• Description: retinol dehydrogenase 12 (all-trans/9-cis/11-cis) [Source:HGNC Symbol;Acc:19977]

Sequence

>retro_amel_673
CTCCATATTCTGATCAACAATGCAGAAGTGATGATGTATCCATACTCCAAGAAAGCTGGTGACTTTGAAACCCACTTGGG
AGTCAACCACCTCAGCCACTTCCTTTGTACCCACTTGCTCCTGGTGCCACTGAAAAAGTGCCCTCACAGGTGATGAACCT
GTCATCAGTAACCCACCATGCTAGCAAGAGTCACTTCCACAACCTCCAGGGTGAGAAACAGTACAGCCGGGGTTTTGCTC
ATTGCCACAGCAAGGTGGCCAATGTATTTTTAATTGGGAACTGGCCAAGAGACTCCAAGGCACAGGGGTCACCACCTATG
CAGTGCACCCAGGCATCATCTGCTCCCAACTGGTCTGGCACTCCTTCCTGCTATGTCTGCTCTGGGGGTTCTTCTCCCCC
TTCATCAAGTCAACACGGTAGGGGGCATGGACCAGGTTGCATTGTGCTTTAGCTGAGAGCCTGGAGCCCCTGTGTGGGAA
GAACTTTGGTGACTGCAAGAGGACCTGGGTGTCCTCAAGTGTCTAAAATAGCAAAACCATTGAGTGCCTGTGGAATGTCG
CTGGGAGCTTCTAAAAATACAGTGGGAG

Alignment

ORF - retro_amel_673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.15 %
• Parental protein coverage: 61.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LHILINNAGVMMCPYSKTADGFESHLGVNHLGHFLLTHLLLERLKESTPAR-VVNLSSVVHHAGKIHFHD
          LHILINNA.VMM.PYSK.A..FE.HLGVNHL.HFL.THLLL..LK...P.R.V.NLSSV.HHA.K.HFH.
Retrocopy LHILINNAEVMMYPYSKKAGDFETHLGVNHLSHFLCTHLLLVPLKK-CPHR<VMNLSSVTHHASKSHFHN

Parental  LQSEKYYSRSLAYCHSKLANV-LFTRELAKRLQGTGVTTYAVHPGIVSSELVRHSFLLCLLWRIFSPFIK
          LQ.EK.YSR..A.CHSK.ANV..F..ELAKRLQGTGVTTYAVHPGI..S.LV.HSFLLCLLW..FSPFIK
Retrocopy LQGEKQYSRGFAHCHSKVANV<IFNWELAKRLQGTGVTTYAVHPGIICSQLVWHSFLLCLLWGFFSPFIK

Parental  SAWEGAQTSLHCALAEGLEPLSGKYFSDCKKAWVSPKSRDNKTAERLWNVS-CELLGIQWQ
          S...GA.T.LHCALAE.LEPL.GK.F.DCK..WVS......KT.E.LWNV...ELL.IQW.
Retrocopy STR*GAWTRLHCALAESLEPLCGKNFGDCKRTWVSSSV*NSKTIECLWNVA<WELLKIQWE

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_673 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_673 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 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003306	1 retrocopy	retro_amel_114,
Ailuropoda melanoleuca	ENSAMEG00000008036	1 retrocopy	retro_amel_673 ,
Canis familiaris	ENSCAFG00000016446	1 retrocopy	retro_cfam_2068,
Felis catus	ENSFCAG00000014092	1 retrocopy	retro_fcat_1910,
Loxodonta africana	ENSLAFG00000022637	1 retrocopy	retro_lafr_847,
Macropus eugenii	ENSMEUG00000001473	1 retrocopy	retro_meug_41,
Meleagris gallopavo	ENSMGAG00000011960	1 retrocopy	retro_mgal_16,
Microcebus murinus	ENSMICG00000010855	1 retrocopy	retro_mmur_432,
Ornithorhynchus anatinus	ENSOANG00000015759	1 retrocopy	retro_oana_89,
Procavia capensis	ENSPCAG00000009359	1 retrocopy	retro_pcap_1,
Pelodiscus sinensis	ENSPSIG00000010721	1 retrocopy	retro_psin_24,
Sarcophilus harrisii	ENSSHAG00000012445	1 retrocopy	retro_shar_41,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,