RetrogeneDB ID: retro_meug_287

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: GeneScaffold_951:16395..17049(-)
• Located in intron of: ENSMEUG00000003357

Retrocopy information

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

Parental gene information

• Parental gene symbol: THYN1
• Ensembl ID: ENSMEUG00000008297
• Aliases: None
• Description: thymocyte nuclear protein 1 [Source:HGNC Symbol;Acc:29560]

Sequence

>retro_meug_287
ATGCCGAGGCCACGGAAGAGAGCCTCCCGGTGTGCACCCGAGCCAGAAATGGAGGCTCTATCAGGCAAATGTGTCAAGGC
CACCAAGACTGAGACCCTACACAAGCCAGTGGTAGAAGCAAAGACCTGTGACTCCCCAGAGAAGGATCGAGCCACTAAAA
ATTGTGGAAAGGAGCCAAGTGGTTACTGGCTGATGAAATCAGAGCCAGAAAGCCGGCTGGAGAAGGGCATAGATGTGAAG
TTTGGCATCAAGGATCTCAAAGCACAGCCTAAACAGACAGCATGCTGGGATGGTGTTCGAAACTATCAGGCCCGGAACTT
CCTGAGAGCAATGAAACTGGGAGAGCAGGCCTTCTTCTATCACAGCAACTGTGAGGAACCAGGCATCGCAGGCCTCATGA
AGATTGTGAAGGAGGCCTACCCTGACCACACACAATTTGAGAAAAATATCCCTCATTATGACCCATCCAGCAAGAAGGAC
AACCCCAAGTGGTCCATGGTGGATGTCCAGTTTATTCGAATGACCAAACGTTTTATTCCCCTGGCTGAACTCAAGGTGCA
TCACCAGGCCCACAAAGCCAACGGTGGCCCTTTAGAAAACATGGCTCTCTTCACCCGTCAGAGACTGTCAGTACAGCCCT
TGACCCAAGGTGAG

Alignment

ORF - retro_meug_287 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.45 %
• Parental protein coverage: 94.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPRPRKRASRCAPEPEMEAPSGKCVKATKTETLHKPVVEAKTCDSPEK-RATKL--KEPSGYWLMKSXXX
          MPRPRKRASRCAPEPEMEA.SGKCVKATKTETLHKPVVEAKTCDSPEK.RATK...KEPSGYWLMKS...
Retrocopy MPRPRKRASRCAPEPEMEALSGKCVKATKTETLHKPVVEAKTCDSPEKDRATKNCGKEPSGYWLMKSEPE

Parental  XXXXXXXXXXFGIEDLKAQPKQTACWDGVRNYQARNFLRAMKLGEEAFFYHSNCKEPGIAGLMKIVKEAY
          ..........FGI.DLKAQPKQTACWDGVRNYQARNFLRAMKLGE.AFFYHSNC.EPGIAGLMKIVKEAY
Retrocopy SRLEKGIDVKFGIKDLKAQPKQTACWDGVRNYQARNFLRAMKLGEQAFFYHSNCEEPGIAGLMKIVKEAY

Parental  PDHTQFEKNSPHYDPSSKKDNPKWSMVDVQFIRMTKRFIPLAELKVHHQAHKANGGPLENMALFTRQRLS
          PDHTQFEKN.PHYDPSSKKDNPKWSMVDVQFIRMTKRFIPLAELKVHHQAHKANGGPLENMALFTRQRLS
Retrocopy PDHTQFEKNIPHYDPSSKKDNPKWSMVDVQFIRMTKRFIPLAELKVHHQAHKANGGPLENMALFTRQRLS

Parental  VQPLTQEE
          VQPLTQ.E
Retrocopy VQPLTQGE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_287 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_287 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii 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,