RetrogeneDB ID: retro_amel_114

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192410.1:1338340..1338961(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000019881
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RDH13
• Ensembl ID: ENSAMEG00000003306
• Aliases: None
• Description: retinol dehydrogenase 13 (all-trans/9-cis) [Source:HGNC Symbol;Acc:19978]

Sequence

>retro_amel_114
TTAAAGGAAGAACCTAGACTGGATGTCTTAATCAACAATGCAGGGATCTTCCAGTGCCCTTATATGAAGACTGAAGATGG
GTTTGAGATGCAGTTTGGAGTGAACCATCTGGGGCACTTCCTACTCACCAATCTTCTCCTTGGACTCCTCAAAAGTTCAG
CTCCCAGCAGGATTGTGGTAGTTTCTTCCAAACTTTATAAATATGGAGACATCAACTTTGAAGACTTGAACAGTGAACAG
AGTTATAATAAAAGCTTTTGTTATAGTCGGAGCAAACTGGCTAACATTCTTTTTACCAGAGAACTAGCCCGCCGCTTAGA
AGGCACAAACGTGACTGTCAACGTATTACACCCTGGCATTGTGCGGACAAATCTTGGCAGGCACATACACATGCCACTGT
TGGTCAAACCACTTTTCAATTTGGTGTCATGGGCTTTTTTCAAAACCCCATTAGAAGGTGCCCAGACTTCGGTTTATTTA
GCCTCTTCACCTGAGGTAGATGGTGTGTCAGGAAAGTACTTTGGAGATTGTAAAGAGGAAGAACTATTGCCCAAAGCTAT
GGATGAGTCTGTTGCAAGAAAACTCTGGGATATCAGTGAAGTAATGGTTGGCATATTAAAA

Alignment

ORF - retro_amel_114 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.59 %
• Parental protein coverage: 61.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEGQVHILVNNAAVMRCPHWTTEDGFEMQFGVNHLGHFLLTNLLLDTLKASAPSRIINLSSLAHVAGHI
          .EE.....L.NNA....CP...TEDGFEMQFGVNHLGHFLLTNLLL..LK.SAPSRI...SS.....G.I
Retrocopy KEEPRLDVLINNAGIFQCPYMKTEDGFEMQFGVNHLGHFLLTNLLLGLLKSSAPSRIVVVSSKLYKYGDI

Parental  DFDDLNWEKRKYDTKAAYCQSKLAVILFTKELSRRLQGTGVTVNALHPGVARTELGRHTGMHSSAFSSFT
          .F.DLN.E...Y.....Y..SKLA.ILFT.EL.RRL.GT.VTVN.LHPG..RT.LGRH..M.......F.
Retrocopy NFEDLNSE-QSYNKSFCYSRSKLANILFTRELARRLEGTNVTVNVLHPGIVRTNLGRHIHMPLLVKPLFN

Parental  LGPIFWLLVKSPELAAQPSTYLAVAEELGGVSGKYFDGLKEKPPAPEAEDEEVAQRLWAESARLVGL
          L....W...K.P...AQ.S.YLA...E..GVSGKYF...KE....P.A.DE.VA..LW..S...VG.
Retrocopy L--VSWAFFKTPLEGAQTSVYLASSPEVDGVSGKYFGDCKEEELLPKAMDESVARKLWDISEVMVGI

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_114 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_114 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003306	1 retrocopy	retro_amel_114 ,
Ailuropoda melanoleuca	ENSAMEG00000008036	1 retrocopy	retro_amel_673,
Equus caballus	ENSECAG00000023146	1 retrocopy	retro_ecab_338,
Ochotona princeps	ENSOPRG00000015998	2 retrocopies	retro_opri_286, retro_opri_524,
Petromyzon marinus	ENSPMAG00000009095	1 retrocopy	retro_pmar_3,
Pongo abelii	ENSPPYG00000010398	1 retrocopy	retro_pabe_1972,
Pan troglodytes	ENSPTRG00000011484	1 retrocopy	retro_ptro_1576,
Sorex araneus	ENSSARG00000003600	1 retrocopy	retro_sara_314,
Tupaia belangeri	ENSTBEG00000016531	1 retrocopy	retro_tbel_1570,
Drosophila melanogaster	FBgn0033203	1 retrocopy	retro_dmel_79,