RetrogeneDB ID: retro_amel_1098

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192902.1:1111149..1111680(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000017345
• Aliases: None
• Description: None

Sequence

>retro_amel_1098
GTGAGTGTGGTTCTGGTTGGTGAGAAAGCTGCGAGTCACTCCTCCATCCTCAACAAAACCAGGGCAGCTGCAGGTGTGGG
AATCACCGCAGCACTGTGAAACCAGCTTCAGTTTCAGAGGAAGAACTGTTGAACTGAAGCCATAAACTAAATAATGATAA
TGTAGGTGGCCTCCTTGTTCAGCTGCCTCTTCCAGAGCACACTGCCGAGGGAGAGATCTGTAATGCGGTTTCTCCAGACA
AGGATGTGGATGGCTTTCACGTCATTCATGTAGGGCGAATGCGTTTGGATCAGTACTCCATGTTACCGACGACCTCAGGA
ATGTCTAGGAAATAATGAAGCAAACTGGCCTTCCAACCCCAGGGAAGAATGTGGTTGTGGCTGGGAGGTCAAAAATGTTG
GAATGCCCATTGCGATGCTACGACGCACAGATGGGGCGCATGAATGACCTGGAGATGATGAGATTATAATATCTCATCCG
TACACTCTATACACACCCAAACATACAGTTCTGGCAGATACTGTGGTCTCT

Alignment

ORF - retro_amel_1098 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.76 %
• Parental protein coverage: 50.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSVVLVGENPASHSYVLN-KTRAAAEVGINSETIVKPASISEEELLNLINKLNNDDNVDGLLVQLPLPEH
          .SVVLVGE..ASHS..LN.........G.N....VKPAS.SEEELLN...KLNND.NV.GLLVQLPLPEH
Retrocopy VSVVLVGEKAASHSSILN<QNQGSCRCG-NHRSTVKPASVSEEELLN*SHKLNND-NVGGLLVQLPLPEH

Parental  IDERKICNAVSPDKDVDGFHVINVGRMCLDQYSMLPATPW-GVWEIIQRTGIPTLGKNVVVAGRS-KNVG
          ..E..ICNAVSPDKDVDGFHVI.VGRM.LDQYSMLP.T....V.EI...TG.PT.GKNVVVAGRS.KNVG
Retrocopy TAEGEICNAVSPDKDVDGFHVIHVGRMRLDQYSMLPTTSG<NV*EIMKQTGLPTPGKNVVVAGRS<KNVG

Parental  MPIAMLLHTDGAHERPGGDATVTISHRYT---PKEQLKKHTVLA
          MPIAML..TDGAHE.PG.D....ISH.YT...PK......TV..
Retrocopy MPIAMLRRTDGAHE*PGDD-EIIISHPYTLYTPKHTVLADTVVS

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_1098 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1098 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 12 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017345	2 retrocopies	retro_amel_1098 , retro_amel_1584,
Canis familiaris	ENSCAFG00000008716	1 retrocopy	retro_cfam_580,
Callithrix jacchus	ENSCJAG00000017810	3 retrocopies	retro_cjac_2225, retro_cjac_2568, retro_cjac_3078,
Homo sapiens	ENSG00000065911	5 retrocopies	retro_hsap_2732, retro_hsap_2817, retro_hsap_3002, retro_hsap_3309, retro_hsap_3874,
Macropus eugenii	ENSMEUG00000013987	4 retrocopies	retro_meug_1468, retro_meug_152, retro_meug_1577, retro_meug_2074,
Mustela putorius furo	ENSMPUG00000007829	3 retrocopies	retro_mputfur_1087, retro_mputfur_1397, retro_mputfur_1551,
Nomascus leucogenys	ENSNLEG00000000326	5 retrocopies	retro_nleu_1196, retro_nleu_207, retro_nleu_2501, retro_nleu_595, retro_nleu_749,
Otolemur garnettii	ENSOGAG00000009089	1 retrocopy	retro_ogar_3390,
Pongo abelii	ENSPPYG00000012283	3 retrocopies	retro_pabe_2271, retro_pabe_2729, retro_pabe_3077,
Pan troglodytes	ENSPTRG00000012081	4 retrocopies	retro_ptro_1846, retro_ptro_1910, retro_ptro_2162, retro_ptro_2641,
Pteropus vampyrus	ENSPVAG00000013948	2 retrocopies	retro_pvam_1357, retro_pvam_1414,
Rattus norvegicus	ENSRNOG00000010833	1 retrocopy	retro_rnor_2170,