RetrogeneDB ID: retro_amel_1156

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192970.1:756540..756847(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TESC
• Ensembl ID: ENSAMEG00000012517
• Aliases: None
• Description: tescalcin [Source:HGNC Symbol;Acc:26065]

Sequence

>retro_amel_1156
TCATTAGACCAGATCCAGTGGCTCAAGTGGAGTTTTAAGCAGCTAAGTGGAGATCAGCCCACTATTCCTAAAGAGGACCT
CAACAAAGTCCCTGACCTAGAATTCAATCTGATGCGAATCAGAATCCACCATGCCTTCTTTGGCAACAGGAGCCTTGGCA
AAGGATCCATCTGTCTGGCTCACAAGATCAACTCTGAGCACTTCCTGACCCAACATGTCGTACTTCTGACCCATCCACGT
CACCAAGGAGAAAGAGCAGGTATAGCTATGCTAAAAAGAAAAGCTGAGATTTTTGTTTTACATGTAT

Alignment

ORF - retro_amel_1156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.08 %
• Parental protein coverage: 52.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSDQIEQLHRRFKQLSGDQPTIRKENFNNVPDLELNPIRSKIVRAFFDNRNLRKGSSGLADEINFEDFLT
          S.DQI..L...FKQLSGDQPTI.KE..N.VPDLE.N..R..I..AFF.NR.L.KGS..LA..IN.E.FLT
Retrocopy SLDQIQWLKWSFKQLSGDQPTIPKEDLNKVPDLEFNLMRIRIHHAFFGNRSLGKGSICLAHKINSEHFLT

Parental  -IMSYFRPIDTTMDEEQVQLCRKEKLRFLFHMY
          ..MSYF.PI..T...EQV.LC.KEKLRFLF.MY
Retrocopy >NMSYF*PIHVTKEKEQV*LC*KEKLRFLFYMY

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_1156 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1156 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012517	1 retrocopy	retro_amel_1156 ,
Canis familiaris	ENSCAFG00000009300	1 retrocopy	retro_cfam_1310,
Equus caballus	ENSECAG00000011177	1 retrocopy	retro_ecab_1005,
Felis catus	ENSFCAG00000002633	1 retrocopy	retro_fcat_1841,
Myotis lucifugus	ENSMLUG00000001775	1 retrocopy	retro_mluc_531,
Mus musculus	ENSMUSG00000029359	1 retrocopy	retro_mmus_212,
Rattus norvegicus	ENSRNOG00000001128	1 retrocopy	retro_rnor_244,