RetrogeneDB ID: retro_amel_875

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192703.1:1329396..1329887(+)
• Located in intron of: ENSAMEG00000010124

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C3
• Ensembl ID: ENSAMEG00000006624
• Aliases: None
• Description: None

Sequence

>retro_amel_875
AACCAAGAACCTGCTATATGTGTGAACGTGAGGTCAGGGATCCAAAGAGTTCAGTTCACGTCAAGAACCCTCTAAGAGAG
GAAGTTATCTGTGGTCTTATCAGAGAAGGACCTGGCACCCTTCAGATAATAACAGAGTCAACATGACACTAAGTAGATTT
TCCCTCAAAGGGAAAGGATGCCCAACATGTCATAATACCATTGACAACTATAAGCTGGTTACAAACGGAGGTCAAAAAGC
ATTACTGCAGCTACAGGGAAAAGGTTATGCTCCTAAAATTGACCCTGTCCCTAAAACAGAAGAGAAGCACCTTGCATGGT
TAAACAGTACCCTCGATCACAGGGTTTGCTCGTTGAACAAGCTCTACGAAAAGCTAAACTGAAAGAAATTGTGGCAGAAT
CTGATGTATGTTCAAGGAAGGATATGAGAATGTCTTTGATAAGCTCCAACAACACAGTCTCCCTGTGTTCAAATTTTCAG
CTGGTATGGGT

Alignment

ORF - retro_amel_875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.94 %
• Parental protein coverage: 55.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NQDSAVHVKMMPEFQR-SSVRIKNPARVEEIICGLIKGGAPKLQIITD-FDMTLSRFSYEGKRCPTCHYV
          NQ..A..V......QR.SSV..KNP.R.EE.ICGLI..G...LQIIT....MTLSRFS..GK.CPTCH..
Retrocopy NQEPAICVNVRSGIQR<SSVHVKNPLR-EEVICGLIREGPGTLQIITE<VNMTLSRFSLKGKGCPTCHNT

Parental  IDSSKLVTDECRKKLLQLKEKYYAIEIDPGLTMEEKY-PYMVEWYTKSHGLLVEQALPKAKLKEIVAESD
          ID..KLVT....K.LLQL..K.YA..IDP....EEK..P.MV..Y..S.GLLVEQAL.KAKLKEIVAESD
Retrocopy IDNYKLVTNGGQKALLQLQGKGYAPKIDPVPKTEEKH<PCMVKQYPRSQGLLVEQALRKAKLKEIVAESD

Parental  V-MLKEGYENFFDKLQQYGIPVFIFSAGIG
          V.M.KEGYEN.FDKLQQ...PVF.FSAG.G
Retrocopy V<MFKEGYENVFDKLQQHSLPVFKFSAGMG

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_875 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_875 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005754	1 retrocopy	retro_amel_1542,
Ailuropoda melanoleuca	ENSAMEG00000006624	1 retrocopy	retro_amel_875 ,
Bos taurus	ENSBTAG00000016709	1 retrocopy	retro_btau_1465,
Canis familiaris	ENSCAFG00000003154	1 retrocopy	retro_cfam_1295,
Equus caballus	ENSECAG00000011777	1 retrocopy	retro_ecab_1118,
Homo sapiens	ENSG00000122643	1 retrocopy	retro_hsap_3084,
Gorilla gorilla	ENSGGOG00000028164	1 retrocopy	retro_ggor_2119,
Mustela putorius furo	ENSMPUG00000005546	2 retrocopies	retro_mputfur_1175, retro_mputfur_577,
Pteropus vampyrus	ENSPVAG00000013182	2 retrocopies	retro_pvam_148, retro_pvam_706,
Rattus norvegicus	ENSRNOG00000005981	1 retrocopy	retro_rnor_632,
Sus scrofa	ENSSSCG00000022912	1 retrocopy	retro_sscr_540,
Ictidomys tridecemlineatus	ENSSTOG00000026363	2 retrocopies	retro_itri_1325, retro_itri_682,