RetrogeneDB ID: retro_amel_278

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192373.1:1604294..1605037(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5DC2
• Ensembl ID: ENSAMEG00000008538
• Aliases: None
• Description: 5'-nucleotidase domain containing 2 [Source:HGNC Symbol;Acc:25717]

Sequence

>retro_amel_278
TTTGACTCTGACGTCATGCTGGCATAGTACACAGAGGCACTAAATGGGGGATGTTCAGTGCCACATCGAGACATTCTGAT
TGAGCACAAATACTCAGAGGGGATTCAAAGGTATGACTACCACTCCAACTTTGCTATATGCATGCTCCAAGGCATTCATA
AGGGCCTCCAGATAAAGACAGAGACCTTCCATTATGTGCAACTGGGTACTACCTACAGTGGCCTCTAATTGTGCAGGACC
AGGAGGTGACCGATCTATACTGGGGCACCTCGCATACTCCACTGCAGCAGACTGGTGGCTTCTAGAGCAAAAGGCCCTCC
ATCCAGTAGTTCACTGACATCTCTCTGCTGCCAGAGATGGCACTGCTCTCCTGCCTGGTGGACCACTCCCTGGCCCATGA
CATGGAGTCCGTCCAAGTGAGTCTTTACAAGGATGTGATATATGTTGGTTGAGATGTGCCATAAAGGGTCTCATATACCA
GCGGATCCAGCAAGACATGGAGAAGTTCCTCCTGAGAGAGGAGGAAATCTTTGCAATCTTGAGCAGCCTGGTGGCCCATG
GGAAACAGGTGGCCCTCCTCACCAACAGTCCCTTCAGCTTCATGGACGAGGTGATGTAACACACGCTGGTCTCAAATGGT
GTCAACTCTTCAAAGAGGTCATTGCCCAGGTGGACAAGCACAGATTTTTCACTGACAGGTAGAAGCCTTTCAGAAATTCA
ATGGGAAGTTCTCCCACCAGTGG

Alignment

ORF - retro_amel_278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.86 %
• Parental protein coverage: 51.65 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FDYDYTLAQYADALHPEIFSAARDILIEHYKYPEGIRKYDYDPSFAIRGLHYDIQKSLLMKIDAFHYVQL
          FD.D..LA.Y..AL........RDILIEH.KY.EGI..YDY...FAI..L...I.K.L..K...FHYVQL
Retrocopy FDSDVMLA*YTEALNGGCSVPHRDILIEH-KYSEGIQRYDYHSNFAICMLQ-GIHKGLQIKTETFHYVQL

Parental  GTAYRGL-QPVPDEEVIDLYGGTQHIPLYQMSGFYGKGPSIKQFMDIFSLPEMALLSCVVDHFLGHGLEF
          GT.Y.GL...V.D.EV.DLY.GT.H.PL.Q..GF..K.PSI..F.DI..LPEMALLSC.VDH.L.H..E.
Retrocopy GTTYSGL<LIVQDQEVTDLYWGTSHTPLQQTGGF*SKRPSIQ*FTDISLLPEMALLSCLVDHSLAHDMES

Parental  DQAHLYKDVTDAIRDV-HVKGLMYQWIERDMEKYILRGDETFAVLSRLVAHGKQLFLITNSPFSFVDKGM
          .Q..LYKDV.....DV...KGL.YQ.I..DMEK..LR..E.FA.LS.LVAHGKQ..L.TNSPFSF.D..M
Retrocopy VQVSLYKDVIYVG*DV<AIKGLIYQRIQQDMEKFLLREEEIFAILSSLVAHGKQVALLTNSPFSFMDEVM

Parental  RHMV-GPDWRQLFDVVIVQADKPSFFTDRRKPFR-KLDEKGSLHW
          .H...G..W.QLF..VI.Q.DK..FFTDR.KPFR.K...K.S..W
Retrocopy *HTL<GLKWCQLFKEVIAQVDKHRFFTDR*KPFR<KFNGKFSHQW

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_278 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_278 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008538	1 retrocopy	retro_amel_278 ,
Canis familiaris	ENSCAFG00000009184	1 retrocopy	retro_cfam_418,
Equus caballus	ENSECAG00000015835	1 retrocopy	retro_ecab_805,
Myotis lucifugus	ENSMLUG00000015418	1 retrocopy	retro_mluc_1559,
Tursiops truncatus	ENSTTRG00000008562	1 retrocopy	retro_ttru_1120,