RetrogeneDB ID: retro_tbel_2414

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_110307:1221..2106(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDAD1
• Ensembl ID: ENSTBEG00000005270
• Aliases: None
• Description: SDA1 domain containing 1 [Source:HGNC Symbol;Acc:25537]

Sequence

>retro_tbel_2414
GAGGTATTTAACTTTTTAGCTATTCACTTGATTCATGATCCCCAAGATTTTGCAGAAAAACTACTAAAGCAGCTGGAGAG
CTCTAAAGAGAGGTTTGAAGTGAAAATGATGCTCATGAACCTCATCTCCAGATTGGTGGGAATTCATGAGCTTTTTCTCT
TCAACTTCTATCCCTTTGTACAAAGGTTCCTGCAGCCCCACCAAAGAGAAGTAACAAAGATCCTTCTGTTTGCTGCCCAA
GCCTCTCATCATCTGGTACCACCAGAGATCATTCACTCACTGCTCATGACTGTGGTCAACAATTTTGTCACTGACAAGAA
CTCTGGGGAAGTCATGACAGTGGGAATCAATGCTATAAAAGAAATAACAGCTCAATGTCCTCTAGCCATGATGGAAGTAC
TTCTCCAAGACCTGGCTCATTATAAAACACACAAAGATAAGAATGTAAAGGTGTCTCCTAGAACTCTGATTTAGCTCTTC
TGAACACTGAATCCTCAGATGTTGCAGAAGAAATTTTGGGTAAAGTCTACAGAGGCTTCCAGAGAAGCAAGAGTGCAAGA
ATATGGAGAATTGGATGCTAAAGATTACATTCCAGGAGCAGAAGTTCTGAAAGTTGAGAAAGAGAATGCTGAAAACGATG
GATGGGAAAGTACCAGTCTCAGTGAGGAGGAGGATGACGATGGCGAGTGGGTTGATGTGCACCACTCCTCCGATGAAGAA
CAGCAAGAAATTGCCAAGAAGCTGAGCAGCATGCTTATGGAGGAGCGGAAAGCCAAGGCTGAAGCCATCAGCACGAGTCG
AGTTTTAATACAGGAAGACTTCCAGAAAATCCTCATGGCCCAGATGAGGAAAGAACTTGATGCTGCCACTGGGAAAGCTC
AAAAG

Alignment

ORF - retro_tbel_2414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.94 %
• Parental protein coverage: 59.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVFNFSAIHLIHDPQDFAEKLLKQLESSKERFEVKMMLMNLISRLVGIHELFLFNFYPFVQRFLQPHQRE
          EVFNF.AIHLIHDPQDFAEKLLKQLESSKERFEVKMMLMNLISRLVGIHELFLFNFYPFVQRFLQPHQRE
Retrocopy EVFNFLAIHLIHDPQDFAEKLLKQLESSKERFEVKMMLMNLISRLVGIHELFLFNFYPFVQRFLQPHQRE

Parental  VTKILLFAAQASHHLVPPEIIHSLLMTVANNFVTDKNSGEVMTVGINAIKEITARCPLAMTEELLQDLAQ
          VTKILLFAAQASHHLVPPEIIHSLLMTV.NNFVTDKNSGEVMTVGINAIKEITA.CPLAM.E.LLQDLA.
Retrocopy VTKILLFAAQASHHLVPPEIIHSLLMTVVNNFVTDKNSGEVMTVGINAIKEITAQCPLAMMEVLLQDLAH

Parental  YKTHKDKNVMMSARTLIQLFRTLNPQMLQKKFRGKPTEASREARVQEYGELDAKDYIPGAEVLEVEKEEN
          YKTHKDKNV..S.RTLI.LF.TLNPQMLQKKF..K.TEASREARVQEYGELDAKDYIPGAEVL.VEKE.N
Retrocopy YKTHKDKNVKVSPRTLI*LF*TLNPQMLQKKFWVKSTEASREARVQEYGELDAKDYIPGAEVLKVEKE-N

Parental  AENGEDGWESTSLSEEEDDDGEWVDVHHSSDEEQQEIAKKLSSMPMEERKAKAAAISTSRV-TQEDFQKI
          AEN..DGWESTSLSEEEDDDGEWVDVHHSSDEEQQEIAKKLSSM.MEERKAKA.AISTSRV..QEDFQKI
Retrocopy AEN--DGWESTSLSEEEDDDGEWVDVHHSSDEEQQEIAKKLSSMLMEERKAKAEAISTSRVLIQEDFQKI

Parental  RLAQMRKELDAAPGKAKR
          ..AQMRKELDAA.GKA..
Retrocopy LMAQMRKELDAATGKAQK

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_2414 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2414 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
Cavia porcellus	ENSCPOG00000008524	2 retrocopies	retro_cpor_510, retro_cpor_994,
Homo sapiens	ENSG00000198301	2 retrocopies	retro_hsap_2412, retro_hsap_4030,
Gorilla gorilla	ENSGGOG00000006441	1 retrocopy	retro_ggor_1498,
Loxodonta africana	ENSLAFG00000012217	1 retrocopy	retro_lafr_980,
Macaca mulatta	ENSMMUG00000017503	1 retrocopy	retro_mmul_604,
Nomascus leucogenys	ENSNLEG00000027034	1 retrocopy	retro_nleu_2410,
Oryctolagus cuniculus	ENSOCUG00000026953	1 retrocopy	retro_ocun_547,
Pongo abelii	ENSPPYG00000014852	1 retrocopy	retro_pabe_1777,
Pan troglodytes	ENSPTRG00000024399	2 retrocopies	retro_ptro_1388, retro_ptro_2732,
Rattus norvegicus	ENSRNOG00000022229	2 retrocopies	retro_rnor_1381, retro_rnor_1967,
Tupaia belangeri	ENSTBEG00000005270	1 retrocopy	retro_tbel_2414 ,