RetrogeneDB ID: retro_amel_979

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192790.1:949479..950013(-)
• Located in intron of: ENSAMEG00000001537

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_979
TTCCTGGAGCCATGCTTTTCTGTGTTTCTCAGCATCTTTTCTTCCTGGAGCTGGCAACGGGGATCCTGGCCTTCATATGC
AAGGACTGGATTCGAGACCAGCTCAGTTTCTTCTGTCAATAACAATGTCAGGGCCTGTCAGGACGACATTGACCTTCAGA
ATCTCTTTGCTCAGAAATATTAGCTTTGCTGTGGAGCCCGAGGGCCTAATGGTTGGCACCTCAATCTGTATTTCAACTGC
ACTGACTTGAACCTGAGCCAGGAGCGCTGTAGGGTCCCCTTCTCCTGCCGCATCAGGGACCCAGCAGAAGATGTCCTCAG
CACCCAGTGTGGCTACAGTAGGCAGCTCACACTGGCGCTGGAGCAGCGGGGGTCCATCCACACTAAAGACTGCATGGACC
AGTTTGAGAAGTGGGTGCAGGACACCCCCATTGTTGTGACTGGGGTCTTTGTGGGCATCGCCCTCCTCCAGATCTTTGGT
ATCTGCCCGGCCCAGAACCTTGTGAGTGCCATCAAGGCAGTGAGGGCCAGCTGG

Alignment

ORF - retro_amel_979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.73 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FLLKFFSVFLGL-IFFLELATGILAFVFKDWIRDQLNFF-INNNVKAYRDDIDLQNLIDFAQEYWSCCGA
          FL...FSVFL....FFLELATGILAF..KDWIRDQL.FF..NNNV.A..DDIDLQNL..FAQ.Y..CCGA
Retrocopy FLEPCFSVFLSI<LFFLELATGILAFICKDWIRDQLSFF>VNNNVRACQDDIDLQNL--FAQKY*LCCGA

Parental  RGPNDWNLNIYFNCTDLNPSRERCGVPFSCCVRDPAEDVLNTQCGYDVRLKLELEQQGSIHTKGCVGQFE
          RGPN.W.LN.YFNCTDLN.S.ERC.VPFSC..RDPAEDVL.TQCGY...L.L.LEQ.GSIHTK.C..QFE
Retrocopy RGPNGWHLNLYFNCTDLNLSQERCRVPFSCRIRDPAEDVLSTQCGYSRQLTLALEQRGSIHTKDCMDQFE

Parental  KWLQDNLIVVAGVFVGIALLQIFGICLAQNLVSDIKAVKANW
          KW.QD..IVV.GVFVGIALLQIFGIC.AQNLVS.IKAV.A.W
Retrocopy KWVQDTPIVVTGVFVGIALLQIFGICPAQNLVSAIKAVRASW

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_979 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_979 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.

---

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,