RetrogeneDB ID: retro_tbel_4516

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_87279:3689..4346(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LXN
• Ensembl ID: ENSTBEG00000017673
• Aliases: None
• Description: latexin [Source:HGNC Symbol;Acc:13347]

Sequence

>retro_tbel_4516
ATGGAAATCCCGCCAGATCAATTCCCAGCCTCCAGGGTGGCATCGGTGGCAGAGAACTGCATTAACTACCAGCAGGGGAC
CCCCCCACAAGGTGTTTCTGGTGCAGACGGTCAAACAAGCCAGCATAGAGGATGTCCCGGGAAGAGGACATAAGTATCGC
CTTAAATTTTCCATGGAAGAAATTATCCAAAAACAAGTTACAGTGAACTGCACAGCTAAAGTACTTTATCCTCCTGTGGG
CCAAGCTACTGCACCAGAAGTCAACTTTACATTTGAAGGAGAAATTGGAAAGAACCCAGATGAAGAAGATAACACATTTT
ATCAAAGACTCAAGTCCATGAAGGAACCACTAGAAGCACAAAATATTCCAGACAGTTTGGAAACGTATCTCCAGAAATGA
AGCCAGTTCGACACTTAGCCTGGGTTGCCTGTGGTTATATAATATGGCAGAATTCTACAGAAAATACCTGGTATAAAATG
GCAAAGATTCAAACTGTCAAGCAAGTGCAAAGAAATGGCAACTTTATTGAATTAGACTACACTATTCTACTTCATGACAT
TGCATCTCACGAGATTATTCCTTGGCAAATGCAAGTTCTCTGGCATCCACAACATGGTACTGAAGTCAAACATAATAGCC
ATCTGCCAAAGGAAGAA

Alignment

ORF - retro_tbel_4516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 99.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEIPPDHYPASRAASVAENCINYQQGTP-HKVFLVQTVKQASMEDIPGRGHKYRLKFSVEEIIQKKVTVN
          MEIPPD..PASR.ASVAENCINYQQGTP.HKVFLVQTVKQAS.ED.PGRGHKYRLKFS.EEIIQK.VTVN
Retrocopy MEIPPDQFPASRVASVAENCINYQQGTP>HKVFLVQTVKQASIEDVPGRGHKYRLKFSMEEIIQKQVTVN

Parental  CTAEVLYPPVGQATAPEVNFTFEGEIGKNPDEEDNTFYQRLKSMKEPLEAQNIPDS-FGNVSPEMKPVRH
          CTA.VLYPPVGQATAPEVNFTFEGEIGKNPDEEDNTFYQRLKSMKEPLEAQNIPDS.FGNVSPEMKPVRH
Retrocopy CTAKVLYPPVGQATAPEVNFTFEGEIGKNPDEEDNTFYQRLKSMKEPLEAQNIPDS<FGNVSPEMKPVRH

Parental  LAWVACGYIIWQNSTENTWYKMAKIQTVKQVQRNDDFIELDYTILLHDIASQEIIPWQMQVLWHPQYGTK
          LAWVACGYIIWQNSTENTWYKMAKIQTVKQVQRN..FIELDYTILLHDIAS.EIIPWQMQVLWHPQ.GT.
Retrocopy LAWVACGYIIWQNSTENTWYKMAKIQTVKQVQRNGNFIELDYTILLHDIASHEIIPWQMQVLWHPQHGTE

Parental  VKHNSRLPKEQ
          VKHNS.LPKE.
Retrocopy VKHNSHLPKEE

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_4516 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4516 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009336	2 retrocopies	retro_btau_569, retro_btau_860,
Canis familiaris	ENSCAFG00000009096	1 retrocopy	retro_cfam_1863,
Callithrix jacchus	ENSCJAG00000000386	1 retrocopy	retro_cjac_1890,
Homo sapiens	ENSG00000079257	1 retrocopy	retro_hsap_3397,
Gorilla gorilla	ENSGGOG00000003092	1 retrocopy	retro_ggor_2300,
Macaca mulatta	ENSMMUG00000004963	1 retrocopy	retro_mmul_2114,
Nomascus leucogenys	ENSNLEG00000004229	1 retrocopy	retro_nleu_1949,
Pongo abelii	ENSPPYG00000014245	1 retrocopy	retro_pabe_2791,
Pan troglodytes	ENSPTRG00000015571	1 retrocopy	retro_ptro_2308,
Pteropus vampyrus	ENSPVAG00000013608	2 retrocopies	retro_pvam_94, retro_pvam_962,
Tupaia belangeri	ENSTBEG00000017673	3 retrocopies	retro_tbel_2746, retro_tbel_3329, retro_tbel_4516 ,