RetrogeneDB ID: retro_amel_2

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192774.1:287020..287932(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000019068
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000011146
• Aliases: None
• Description: None

Sequence

>retro_amel_2
ATGGATCAGCAACTGAAGAAAAAGGCAAAGACTTGTGGGCAGAAAGGCCTGGGTAGAAGAGCCTTCGGGAGGGATAAGCC
AAGGCCATCTAAGCCACAGCCAGTCCAGCAGGGACTTCTCGACACAACATGGGCCTTAGAAGATGAAGGTCTGTTCTTTG
AGACTAGCCATCTGGTTGTTGGAGAAGACTCCTTCTCTGACTGTTACATAGAATGCATAATAAGAGGTGAGTTTTCCGAA
CCCATTCTGGAAGGAGACTCACTTAAGTCCCCTGACTACCCGGAAGAAGAATCAGAACAAGAGCTTTCGCAACAGGTTCT
CACAGCAAGGTCGCTTCTAGAAAAATCCTTGAAATGCGCACAAAAAGGGACAAAACAAGAACTTCCTCAACAGGCTATTA
GAGAGAATTCACAGCTTGAGTATTCCGAGTATGTAACAGGCAAGAAGTTTCCTCTTGGAGGAATACGCAGCACTGACTTA
TCAGCTCCTAAACAGTTTGCAGAATTTGCTAGAAAGAAGCCAACAAAAGATAAGGAATATGAGACTCCAGAAAGAATTGT
TTGTCCTCACAGTGGATGCCCAAAAAAGTTGAAGAATAGGGCTTCCCTGCGAAAGCATCTCCTTGTCCATGGTCCTCGAG
ATCACGTATGTGCAGAATGTGGGAAAGCATTCAATGAGAGTTCAAAACTGAAAAGACATTTTCTGGTTCATACTGGAGAG
AAGCCATTTCGGTGCACTTTTGAAGGGTGCGGAAAACGCTTTTCCCTGGACTACAATTTGCGTACACACGTCCGGATCCA
CACTGGGGAGAAACGTTTTGTGTGTCCCTTTAAAAGCTGTCACAAGAGGTTTATTCAGTCAAATAACCTGAAAGTTCACA
TCTTAACTCATACAAAGACCAACAAAAATCAA

Alignment

ORF - retro_amel_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.18 %
• Parental protein coverage: 58.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EQIIGENSPPDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMKPRKIKEDDAPRTIACPHKKGCTKMFR
          .Q.I.ENS...YSEY.TGKK.P.GGI...DLS.PKQ.AEFAR.KP.K.KE...P..I.CPH..GC.K...
Retrocopy QQAIRENSQLEYSEYVTGKKFPLGGIRSTDLSAPKQFAEFARKKPTKDKEYETPERIVCPHS-GCPKKLK

Parental  DNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHT
          .....RKHL..HGPR.HVCAECGKAF.ESSKLKRH.LVHTGEKPF.CTFEGCGKRFSLD.NLRTHVRIHT
Retrocopy NRASLRKHLLVHGPRDHVCAECGKAFNESSKLKRHFLVHTGEKPFRCTFEGCGKRFSLDYNLRTHVRIHT

Parental  GDRPYVCPFDGCNKKFAQSTNLKSHILTHAKAKNNQ
          G....VCPF..C.K.F.QS.NLK.HILTH.K...NQ
Retrocopy GEKRFVCPFKSCHKRFIQSNNLKVHILTHTKTNKNQ

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_2 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_2 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 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011146	1 retrocopy	retro_amel_2 ,
Bos taurus	ENSBTAG00000020819	1 retrocopy	retro_btau_91,
Callithrix jacchus	ENSCJAG00000016853	2 retrocopies	retro_cjac_1931, retro_cjac_4045,
Cavia porcellus	ENSCPOG00000020809	2 retrocopies	retro_cpor_1220, retro_cpor_1522,
Equus caballus	ENSECAG00000005805	1 retrocopy	retro_ecab_97,
Homo sapiens	ENSG00000100811	2 retrocopies	retro_hsap_106, retro_hsap_97,
Gorilla gorilla	ENSGGOG00000026332	2 retrocopies	retro_ggor_190, retro_ggor_2,
Mustela putorius furo	ENSMPUG00000002931	1 retrocopy	retro_mputfur_867,
Mus musculus	ENSMUSG00000021264	1 retrocopy	retro_mmus_190,
Nomascus leucogenys	ENSNLEG00000000999	3 retrocopies	retro_nleu_1092, retro_nleu_116, retro_nleu_2225,
Oryctolagus cuniculus	ENSOCUG00000026938	1 retrocopy	retro_ocun_1871,
Otolemur garnettii	ENSOGAG00000006955	4 retrocopies	retro_ogar_1231, retro_ogar_1804, retro_ogar_1857, retro_ogar_289,
Pongo abelii	ENSPPYG00000025949	3 retrocopies	retro_pabe_145, retro_pabe_3616, retro_pabe_534,
Pan troglodytes	ENSPTRG00000006717	3 retrocopies	retro_ptro_3093, retro_ptro_45, retro_ptro_494,