RetrogeneDB ID: retro_amel_28

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193506.1:479612..480191(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000019231
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ARF3
• Ensembl ID: ENSAMEG00000007042
• Aliases: None
• Description: ADP-ribosylation factor 3 [Source:HGNC Symbol;Acc:654]

Sequence

>retro_amel_28
ATGGGTCTACTGAGTTCTAAAAACCCCAAAACCAAGCAAGCCCGGATTCTTCTTCTGGGACTTGACTCAGCTGGGAAGTC
TACCCTCCTTTATAAATTAAAGCTTGCTAAGGATATTACGACCATCCCAACAATAGGTTTCAACGTGGAGGTGATCGAGT
TGGAAAAGAGTCTTTCACTCACTGTCTGGGATGTTGGAGGACAAGAAAAAATGAGAACCGTGTGGGAGTATTACTGTGAG
AACACTGATGGGCTGCTGTATGTTGTGGATAGTACGGACAAGCAGCGACTAGAAGACTCCAGGAGAGAGCTGAAGCACAT
TTTGAAGAATGAACACATTAAAAATGTGCCTGTTGTCCTGTTAGCTAACAAACAGGATGTTCCTGGAGCTCTGACTGCCG
AGGACATCACCAGAATGTTCAGGGTGAAGAAGCTCTGCAGTGACCGGAACTGGTATGTGCAGCCCTGCTGTGCCATCACC
GGGGACGGACTGATGGAGGGGCTCAGGAAATTGACTGGATTTGTGAAAAGCCACGTGAAATCAAGAGGAGACACGTTAGC
ATTCTTTAAGCAGAACTGA

Alignment

ORF - retro_amel_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.6 %
• Parental protein coverage: 90.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEY-KNISFTVWDVGGQDKIRPLWRHYFQN
          K..RIL..GLD.AGK.T.LYKLKL....TTIPTIGFNVE..E..K..S.TVWDVGGQ.K.R..W..Y..N
Retrocopy KQARILLLGLDSAGKSTLLYKLKLAKDITTIPTIGFNVEVIELEKSLSLTVWDVGGQEKMRTVWEYYCEN

Parental  TQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSL-RHRNW
          T.GL..VVDS.D..R....R.EL...L.............ANKQD.P.A..A..IT.......L...RNW
Retrocopy TDGLLYVVDSTDKQRLEDSRRELKHILKNEHIKNVPVVLLANKQDVPGALTAEDITRMFRVKKLCSDRNW

Parental  YIQATCATSGDGLYEGLDWLANQLKN
          Y.Q..CA..GDGL.EGL..L....K.
Retrocopy YVQPCCAITGDGLMEGLRKLTGFVKS

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_28 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_28 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 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004184	1 retrocopy	retro_amel_1639,
Ailuropoda melanoleuca	ENSAMEG00000007042	2 retrocopies	retro_amel_28 , retro_amel_70,
Canis familiaris	ENSCAFG00000008767	1 retrocopy	retro_cfam_119,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Felis catus	ENSFCAG00000000088	2 retrocopies	retro_fcat_2, retro_fcat_59,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Macropus eugenii	ENSMEUG00000005072	7 retrocopies	retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Myotis lucifugus	ENSMLUG00000029846	1 retrocopy	retro_mluc_119,
Macaca mulatta	ENSMMUG00000006968	1 retrocopy	retro_mmul_174,
Mustela putorius furo	ENSMPUG00000014730	1 retrocopy	retro_mputfur_86,
Ochotona princeps	ENSOPRG00000007411	2 retrocopies	retro_opri_13, retro_opri_3,
Petromyzon marinus	ENSPMAG00000000531	1 retrocopy	retro_pmar_5,
Pongo abelii	ENSPPYG00000004473	1 retrocopy	retro_pabe_126,
Pteropus vampyrus	ENSPVAG00000004626	1 retrocopy	retro_pvam_7,
Rattus norvegicus	ENSRNOG00000033155	1 retrocopy	retro_rnor_272,
Rattus norvegicus	ENSRNOG00000048089	1 retrocopy	retro_rnor_2521,
Ictidomys tridecemlineatus	ENSSTOG00000004295	1 retrocopy	retro_itri_175,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,