RetrogeneDB ID: retro_amel_300

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192379.1:301657..302341(+)
• Located in intron of: ENSAMEG00000004027

Retrocopy information

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

Parental gene information

• Parental gene symbol: THYN1
• Ensembl ID: ENSAMEG00000007294
• Aliases: None
• Description: thymocyte nuclear protein 1 [Source:HGNC Symbol;Acc:29560]

Sequence

>retro_amel_300
ATGCCTAGACTGGGGAAGAGGCTGGCTAAGGCTGCGGAGCCTGCGGGGTTGGACAATAAGGGGCCAGTAAGAAGACGAAC
CAAGACTAAGAACTCAGCAGGAGCATCAGCCCAAGTGGATAACTCCAGCCCTCAGAAGGCTTCAGCCTCTAAAGACGGTG
GGCAGAATCTAAGCAGTTACTGGCTGATGATGTCAGAGCCAGGAAGCCGACTAGACAAAGGGAGAGGTGAAGCGCAGCAC
TGGGGATCGCAAAGCACAGCCCGAGCAGACAGCAGGCTGGGATGGGCTTCGCAACTCCCAGGCCCAGAACTTCCTTGAAG
CCCTGAAGCGGGAGGAAGGAGCCTTCTACCAGAGCAACTGTGAAGAACCAGGCATCGCAGGACTTGCGAAGCTTGTGCAG
GAGGCTTGCCCAGACCACCCACAGTTTGAGAACAACAATCCCTATTGTGACCCATCCAGCAAAGAAGGCAACCCCACATG
GCCCAAGGTGGAGGTACAGTTTGTTCAGACGATGAAGGGTTCCATGACGCTGGTGACTGAGCTCAAAACCCATCACCAAA
CCTGCAAAGCTGCTGGAGGCCCCTTAAAAATAGGGCCCTTTCCACTCGCCGGAGACATTGCATTCATCCCCTGACTCAAG
AGGAGTTTGATTTTATTTTGAGGCTGGAGGAAAAGGCACCAAGC

Alignment

ORF - retro_amel_300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.96 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPKPRKRLAGAAGPAGPDNKGPAGKRTKTKNPAGASATMGNSSPEKTSASIDSGKNLSNYWLMKSEPESR
          MP...KRLA.AA.PAG.DNKGP...RTKTKN.AGASA...NSSP.K.SAS.D.G.NLS.YWLM.SEP.SR
Retrocopy MPRLGKRLAKAAEPAGLDNKGPVRRRTKTKNSAGASAQVDNSSPQKASASKDGGQNLSSYWLMMSEPGSR

Parental  LE-KGVDVKFSIEDLKAQPKQTACWDGVRNYQARNFLRAMKLEQEAFFYHSNCKEPGIAGLVKIVKEAYP
          L..KG..VK.S..D.KAQP.QTA.WDG.RN.QA.NFL.A.K.E..AF.Y.SNC.EPGIAGL.K.V.EA.P
Retrocopy LD>KG-EVKRSTGDRKAQPEQTAGWDGLRNSQAQNFLEALKREEGAF-YQSNCEEPGIAGLAKLVQEACP

Parental  DHTQFEKNNPHYDPSSKEDNPKWSIIQVDVQFVRMMKRYITL-AELKTHHQAHKTTGG-PLKNMALFTRQ
          DH.QFE.NNP..DPSSKE.NP.W....V.VQFV..MK...TL..ELKTHHQ..K..GG.PLKN.AL.TR.
Retrocopy DHPQFENNNPYCDPSSKEGNPTWP--KVEVQFVQTMKGSMTLVTELKTHHQTCKAAGG<PLKNRALSTRR

Parental  RLSVQPSLVEEFNFILSLEEKEPS
          R....P...EEF.FIL.LEEK.PS
Retrocopy RHCIHPLTQEEFDFILRLEEKAPS

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_300 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_300 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007294	1 retrocopy	retro_amel_300 ,
Canis familiaris	ENSCAFG00000009772	1 retrocopy	retro_cfam_877,
Cavia porcellus	ENSCPOG00000006567	1 retrocopy	retro_cpor_1542,
Felis catus	ENSFCAG00000007419	1 retrocopy	retro_fcat_946,
Macropus eugenii	ENSMEUG00000008297	1 retrocopy	retro_meug_287,
Mustela putorius furo	ENSMPUG00000009185	1 retrocopy	retro_mputfur_1114,