RetrogeneDB ID: retro_amel_1158

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192976.1:113274..113825(+)
• Located in intron of: ENSAMEG00000003515

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000013985
• Aliases: None
• Description: None

Sequence

>retro_amel_1158
ATAGGCTCGGCCAAGAGCACCCCAGTCACTCCAGCACAGCCTTCACTGCACAAGCTTCTGGCCCAAGTGGTGGAACCCCG
TTTACCCAGAGCCAGCATCCGGCACACTCCGATCTCGGTGGAGAGCCCTCCTCAGCCAAACCTACCAGCAGGGGAGCAGC
TGGAAGGTCCCAATCAGATCCAAGACCCTACCTCTTCTGCCCTTAGCACTGCATAACACCTATGAAGACCAGCAGTAGAG
GGCCCTCAAGCCCACTGGTCAATCAGCTGAGTGAAGTTATTTGAAACGGAAGGCTCCATATCGAATCTTCCCCCAGAGCC
TGTTGTGCCCTTAAAGGTGACTTCATCTTCTGAACTGGACGTGCCTCTGGGTACTAGTTTTCCCTTGAGAACCAGACGCC
ACCCTGGAGCCAGACTGAGCTTCCCTCCAAGCAGGTGTTCTCCAAGGAGGACGCAGGACAGCCCTCAGAAACTCCCGTGA
CTAGCCAGGGCTCAGACAAGCCCTTAAGAGAACCTGAGACTCCCTGATCTTCAGGTTCTCAGCACAATAGA

Alignment

ORF - retro_amel_1158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.63 %
• Parental protein coverage: 69.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGSAKSAPVTPARPPPHNKLLARVADPRSPSAGILRTPIQVESSPQPNLPAGEQLEGPNQAQDSDPRSPT
          .GSAKS.PVTPA.P..H.KLLA.V..PR.P.A.I..TPI.VES.PQPNLPAGEQLEGPNQ.QD..P.S..
Retrocopy IGSAKSTPVTPAQPSLH-KLLAQVVEPRLPRASIRHTPISVESPPQPNLPAGEQLEGPNQIQD--PTSSA

Parental  LGIA-RTPMKTSSGEPPSPLMKQLSEV-FETEAPKSNLPPEPLLPSEATSSSELDLPLGTQF-SLEDQVP
          L..A..TPMKTSS..P.SPL..QLSEV.FETE...SNLPPEP..P...TSSSELD.PLGT.F.SLE.Q.P
Retrocopy LSTA<ITPMKTSSRGPSSPLVNQLSEV>FETEGSISNLPPEPVVPLKVTSSSELDVPLGTSF<SLENQTP

Parental  PWSQTELPSKQVFSKEEAGQPSETPMTGQSSDKPLRDPETPRSSGSKHNR
          PWSQTELPSKQVFSKE.AGQPSETP.T.Q.SDKPLR.PETP.SSGS.HNR
Retrocopy PWSQTELPSKQVFSKEDAGQPSETPVTSQGSDKPLREPETP*SSGSQHNR

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_1158 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1158 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013985	1 retrocopy	retro_amel_1158 ,
Canis familiaris	ENSCAFG00000014650	4 retrocopies	retro_cfam_1100, retro_cfam_1940, retro_cfam_345, retro_cfam_633,
Cavia porcellus	ENSCPOG00000012334	1 retrocopy	retro_cpor_1073,
Felis catus	ENSFCAG00000004274	2 retrocopies	retro_fcat_1182, retro_fcat_1942,
Mustela putorius furo	ENSMPUG00000016781	1 retrocopy	retro_mputfur_663,
Pteropus vampyrus	ENSPVAG00000012300	4 retrocopies	retro_pvam_235, retro_pvam_248, retro_pvam_297, retro_pvam_667,
Rattus norvegicus	ENSRNOG00000015529	1 retrocopy	retro_rnor_2685,
Ictidomys tridecemlineatus	ENSSTOG00000023573	1 retrocopy	retro_itri_804,
Tupaia belangeri	ENSTBEG00000001905	1 retrocopy	retro_tbel_534,
Vicugna pacos	ENSVPAG00000009784	1 retrocopy	retro_vpac_296,