RetrogeneDB ID: retro_amel_391

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192418.1:3048047..3048628(+)
• Located in intron of: ENSAMEG00000016707

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS7
• Ensembl ID: ENSAMEG00000018435
• Aliases: None
• Description: None

Sequence

>retro_amel_391
ATCTTCGGTTCTAGCACGAAGATCGTGAAGCCCTATGGCAGGAAGCTGGATGAGTTCAAGTGCGGCATCTCCCAGCCTGT
CCTTGAGCTGGAGAGGAGCTCGGACCTCAAAGCCCAGTGAAGGGAGCTGAATATAACAGCAGCCAAGGAAATCGAAGTTG
GCGGGGGGTTGGAAGGCTCTTATCATCTTTGTTCCCAGTCCTCAGCTGAAATCTTTCCAGAAAATCCCAGTCCGGCTAGT
CTGTGAATTGGAGAAAAAGTTCAGTGGGAAGCATGTTGTCTTCATTGCTTAGAGAATTCTGCCTCAGCCAACTTGAAAAA
AAGCCATACAAAAAAGGAGCAGAAGGGTCCCAGGATCTGCACTTTGACAGCCGTGCGTGACGCAATCCTGGAGAACATGG
TTTTTCCAAGCGGAATTGTAGGCGAGGTGCTCCACGTGAAGCTGGGTGGCCTCTGCTCACCGAGGTTCATCTGGTTAAAG
CACAGCAGAGTGACCTGGAGCACAAGGTTGAAGCTCTCTCTGGTATCTGTAAGCAGCTCACCAGCAAGGATGTTAACTTG
GAGTTCACAGAGTTTCAGTTG

Alignment

ORF - retro_amel_391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.2 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGR-KAIIIFVPVPQL
          .F.SS.KIVKP.G.K.DEF..GISQ..LELE..SDLKAQ.RELNITAAKEIEVGGG..KA.IIFVP.PQL
Retrocopy IFGSSTKIVKPYGRKLDEFKCGISQPVLELERSSDLKAQ*RELNITAAKEIEVGGGL>KALIIFVPSPQL

Parental  KSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPT-RKSRTK-NKQKRPRSRTLTAVHDAILEDLVFPS
          KSFQKI.VRLV.ELEKKFSGKHVVFIA..RILP.PT..K...K...QK.PR..TLTAV.DAILE..VFPS
Retrocopy KSFQKIPVRLVCELEKKFSGKHVVFIA-*RILPQPT*KKAIQK<KEQKGPRICTLTAVRDAILENMVFPS

Parental  EIVGKRIRVKLDG-SRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL
          .IVG....VKL.G...L..VHL.KAQQ...EHKVE..SG..K.LT.KDVN.EF.EFQL
Retrocopy GIVGEVLHVKLGG<PLLTEVHLVKAQQSDLEHKVEALSGICKQLTSKDVNLEFTEFQL

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_391 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_391 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 11 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018435	2 retrocopies	retro_amel_391 , retro_amel_914,
Callithrix jacchus	ENSCJAG00000016462	2 retrocopies	retro_cjac_16, retro_cjac_2287,
Felis catus	ENSFCAG00000023243	2 retrocopies	retro_fcat_1534, retro_fcat_41,
Gorilla gorilla	ENSGGOG00000023095	13 retrocopies	retro_ggor_2028, retro_ggor_2090, retro_ggor_2161, retro_ggor_218, retro_ggor_2452, retro_ggor_2927, retro_ggor_294, retro_ggor_2965, retro_ggor_3047, retro_ggor_346, retro_ggor_400, retro_ggor_484, retro_ggor_597,
Loxodonta africana	ENSLAFG00000015087	11 retrocopies	retro_lafr_1223, retro_lafr_160, retro_lafr_217, retro_lafr_318, retro_lafr_319, retro_lafr_413, retro_lafr_514, retro_lafr_720, retro_lafr_786, retro_lafr_964, retro_lafr_970,
Myotis lucifugus	ENSMLUG00000006121	1 retrocopy	retro_mluc_1118,
Macaca mulatta	ENSMMUG00000011870	7 retrocopies	retro_mmul_1831, retro_mmul_1846, retro_mmul_1929, retro_mmul_23, retro_mmul_2403, retro_mmul_2540, retro_mmul_357,
Otolemur garnettii	ENSOGAG00000028165	1 retrocopy	retro_ogar_133,
Pan troglodytes	ENSPTRG00000011615	3 retrocopies	retro_ptro_202, retro_ptro_3132, retro_ptro_58,
Pteropus vampyrus	ENSPVAG00000002071	7 retrocopies	retro_pvam_1051, retro_pvam_1183, retro_pvam_1330, retro_pvam_1437, retro_pvam_207, retro_pvam_543, retro_pvam_887,
Sus scrofa	ENSSSCG00000027353	5 retrocopies	retro_sscr_136, retro_sscr_137, retro_sscr_240, retro_sscr_364, retro_sscr_956,