RetrogeneDB ID: retro_amel_1707

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194038.1:141943..142275(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM96A
• Ensembl ID: ENSAMEG00000002448
• Aliases: None
• Description: family with sequence similarity 96, member A [Source:HGNC Symbol;Acc:26235]

Sequence

>retro_amel_1707
GATCCAGAGAAGCCCAATACTTAGAAGAGCTCGAAGTGGTAATGGTAAGTAGTATGGACGTTCAGGAGAGAAAGGATAGC
TATTTGGTTGCTATCAGGTTCAGGCCAACAGTACCTCACTGCTGTTCGGCAACCCTTAGTGGGCTGTGCTTAAGAGTAAA
ACCTCAGTGTTTTTTTACCATTTAAAGGTAAGTTGGAAATCTGCATTTCTGAAGGAACCCACTCAGCAGAGGAAGACAAC
AACAGGAAGATAAATGACAAAGAGCAAGTGGCACTGCAATGGAAAACACTACTTTACAGGAAATCCTGTACTAGTGTATC
CTGGAACCTAAT

Alignment

ORF - retro_amel_1707 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.24 %
• Parental protein coverage: 70.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DPEKPNT-LEELEVVTESSVEVQEINEEDCLVVIRFTPTVPHCSLATLIAGLCLRVK-LQRCLPFKHKLE
          DPEKPNT.LEELEVV..SS..VQE......LV.IRF.PTVPHC..ATL..GLCLRVK.L...LPFK.KLE
Retrocopy DPEKPNT<LEELEVVMVSSMDVQE-RKDSYLVAIRFRPTVPHCCSATL-SGLCLRVK>LSVFLPFKGKLE

Parental  IYISEGTHSTEEDINKQINDKERVA-AAMENPNLREIVEQCVLEPD
          I.ISEGTHS.EED.N..INDKE.VA..AMEN..L.EI...C.LEP.
Retrocopy ICISEGTHSAEEDNNRKINDKEQVA<TAMENTTLQEILY*CILEPN

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_1707 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1707 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 22 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002448	1 retrocopy	retro_amel_1707 ,
Ailuropoda melanoleuca	ENSAMEG00000017164	1 retrocopy	retro_amel_1340,
Bos taurus	ENSBTAG00000002012	2 retrocopies	retro_btau_509, retro_btau_984,
Canis familiaris	ENSCAFG00000017035	2 retrocopies	retro_cfam_1450, retro_cfam_439,
Callithrix jacchus	ENSCJAG00000004834	1 retrocopy	retro_cjac_1751,
Equus caballus	ENSECAG00000010303	1 retrocopy	retro_ecab_364,
Erinaceus europaeus	ENSEEUG00000000854	1 retrocopy	retro_eeur_323,
Felis catus	ENSFCAG00000004178	1 retrocopy	retro_fcat_1379,
Homo sapiens	ENSG00000166797	2 retrocopies	retro_hsap_2763, retro_hsap_522,
Gorilla gorilla	ENSGGOG00000016550	2 retrocopies	retro_ggor_1921, retro_ggor_481,
Loxodonta africana	ENSLAFG00000011114	1 retrocopy	retro_lafr_758,
Macropus eugenii	ENSMEUG00000005979	2 retrocopies	retro_meug_471, retro_meug_85,
Microcebus murinus	ENSMICG00000011072	1 retrocopy	retro_mmur_233,
Myotis lucifugus	ENSMLUG00000028233	2 retrocopies	retro_mluc_578, retro_mluc_893,
Mustela putorius furo	ENSMPUG00000000605	1 retrocopy	retro_mputfur_722,
Mus musculus	ENSMUSG00000032381	1 retrocopy	retro_mmus_1919,
Nomascus leucogenys	ENSNLEG00000026932	3 retrocopies	retro_nleu_156, retro_nleu_2577, retro_nleu_667,
Ochotona princeps	ENSOPRG00000015229	5 retrocopies	retro_opri_476, retro_opri_522, retro_opri_828, retro_opri_84, retro_opri_999,
Pongo abelii	ENSPPYG00000006544	1 retrocopy	retro_pabe_224,
Pan troglodytes	ENSPTRG00000007153	2 retrocopies	retro_ptro_1870, retro_ptro_390,
Sorex araneus	ENSSARG00000002068	3 retrocopies	retro_sara_54, retro_sara_597, retro_sara_742,
Tarsius syrichta	ENSTSYG00000004186	2 retrocopies	retro_tsyr_195, retro_tsyr_62,