RetrogeneDB ID: retro_amel_1365

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193254.1:605093..605616(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPAN17
• Ensembl ID: ENSAMEG00000007218
• Aliases: None
• Description: tetraspanin 17 [Source:HGNC Symbol;Acc:13594]

Sequence

>retro_amel_1365
GTTTTTCTCAGCGTTCATCTCTTCTTCCTGGGGCTGGTAACAGGGATCTTGGCCTTGGTACTGAAGGACTAGATTTGAGA
CCAGCTCAATTTCCTCCTGAACTACAACATCAAGGCCATTGGGACAACATTGACCTCCAGAACTTCATTGACTTTGCTCA
GGAATATCTGTCTTGCTGCAGAGCCTGAGGGCCTAATGACTGGAACTCGATATTTATTTCAACTGCACTGCCTTGAACCC
CAGCCAGGAGTGCTGCAGGATGCTCTTCTCCTGCTATGTCAGGGACCCTGTGGAAGGTGTCCTCAACACTCAGTGTGGCC
AGGACTCCAGGCTCAAACTGGAGCTGGAGCAGCGGGGCTCCATCCACACCAAAGGCTGATGCGTGGGCCAGTTCATGAAG
TGGCTGAGGGACAACCTGATTGTTGTGGCTGGGGTCTTTGTGGCCATCGCCCTCCTCCAGATCTTTGGTATCTGTTTGGC
CCAGAGCCTTGCGAGGGACATCAAGGCAGTGAAGGGCAACTGG

Alignment

ORF - retro_amel_1365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.14 %
• Parental protein coverage: 64.07 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFLGL-IFFLELATGILAFVFKDWIRDQLNFFINNNVKA-YRDDIDLQNLIDFAQEYWSCCGARGPNDWN
          VFL....FFL.L.TGILA.V.KD.I.DQLNF..N.N.KA...D.IDLQN.IDFAQEY.SCC.A.GPNDWN
Retrocopy VFLSVHLFFLGLVTGILALVLKD*I*DQLNFLLNYNIKA<HWDNIDLQNFIDFAQEYLSCCRA*GPNDWN

Parental  -LNIYFNCTDLNPSRERCGVPFSCCVRDPAEDVLNTQCGYDVRLKLELEQQGSIHTKG-CVGQFEKWLQD
          .L.IYFNCT.LNPS.E.C...FSC.VRDP.E.VLNTQCG.D.RLKLELEQ.GSIHTKG.CVGQF.KWL.D
Retrocopy <LDIYFNCTALNPSQECCRMLFSCYVRDPVEGVLNTQCGQDSRLKLELEQRGSIHTKG*CVGQFMKWLRD

Parental  NLIVVAGVFVGIALLQIFGICLAQNLVSDIKAVKANW
          NLIVVAGVFV.IALLQIFGICLAQ.L..DIKAVK.NW
Retrocopy NLIVVAGVFVAIALLQIFGICLAQSLARDIKAVKGNW

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_1365 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1365 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007218	2 retrocopies	retro_amel_1365 , retro_amel_979,
Ailuropoda melanoleuca	ENSAMEG00000013851	1 retrocopy	retro_amel_742,
Canis familiaris	ENSCAFG00000016638	2 retrocopies	retro_cfam_1585, retro_cfam_704,
Callithrix jacchus	ENSCJAG00000007278	1 retrocopy	retro_cjac_2289,
Equus caballus	ENSECAG00000022322	1 retrocopy	retro_ecab_554,
Felis catus	ENSFCAG00000007803	1 retrocopy	retro_fcat_1133,
Mustela putorius furo	ENSMPUG00000012505	1 retrocopy	retro_mputfur_428,