RetrogeneDB ID: retro_tbel_2746

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_118053:145477..146051(-)
• 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_2746
GGGACCCCCCACAGGTGTTCTGGTGCAGATGATCAAACTAGCAGCATGGAAGATAATCTGGGAAGAGGACATAAGTATCG
CATTAAATTTTCCATGGAAGAAATTATCCAAAAAATGTTAAGGTGAGCTGTACAGCTGAAGTACTTATCCTCCTGTGGGA
CAAGTTACTGCACCAGAAGTCAACTTTACATTTGAAGGGGAAATCGGAAAGAATGCAGATGAAGAAAATACATTTTATCA
AAGACTCAAGTCCCATGAAGGAACCACGAGAAGCACAAAATATTCCAGGCAGTTTTGGAAATTATCTCCAGAAATGAAGC
CAGTTCGACATTTAGCCTGGGTTGCCTGTGGTTATATAATATGGCAGAATTCTACAGAAAACACCTGGTATAAAATGGCA
AAGATTCAAACTGCCAAGCAAGTGCAAAGAAATGACGACTTTATTGAATTAGACTACACCATTCTACTTCATGACATTGC
ATCTCAGGAGATGATTCCTTGGCAAATGCAAGTTCTCTGGCATCCACAACATGGTACTAAAGTCAAACATAATAGCCATC
TGCCAAAGGAAGAA

Alignment

ORF - retro_tbel_2746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.57 %
• Parental protein coverage: 87.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GTPHK-VF-LVQTVKQA-SMEDIPGRGHKYRLKFSVEEIIQK-KVTVNCTAEVL-YPPVGQATAPEVNFT
          GTPH..VF.LVQ..K.A.SMED..GRGHKYR.KFS.EEIIQK..V.V.CTAEVL.YPPVGQ.TAPEVNFT
Retrocopy GTPHR<VF<LVQMIKLA<SMEDNLGRGHKYRIKFSMEEIIQK<NVKVSCTAEVL<YPPVGQVTAPEVNFT

Parental  FEGEIGKNPDEEDNTFYQRLKS-MKEPLEAQNIPDSFGN-VSPEMKPVRHLAWVACGYIIWQNSTENTWY
          FEGEIGKN.DEE.NTFYQRLKS.MKEP.EAQNIP.SFGN..SPEMKPVRHLAWVACGYIIWQNSTENTWY
Retrocopy FEGEIGKNADEE-NTFYQRLKS>MKEPREAQNIPGSFGN<LSPEMKPVRHLAWVACGYIIWQNSTENTWY

Parental  KMAKIQTVKQVQRNDDFIELDYTILLHDIASQEIIPWQMQVLWHPQYGTKVKHNSRLPKEQ
          KMAKIQT.KQVQRNDDFIELDYTILLHDIASQE.IPWQMQVLWHPQ.GTKVKHNS.LPKE.
Retrocopy KMAKIQTAKQVQRNDDFIELDYTILLHDIASQEMIPWQMQVLWHPQHGTKVKHNSHLPKEE

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_2746 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2746 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,