RetrogeneDB ID: retro_tbel_3536

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_143877:245..1101(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNW1
• Ensembl ID: ENSTBEG00000014074
• Aliases: None
• Description: SNW domain containing 1 [Source:HGNC Symbol;Acc:16696]

Sequence

>retro_tbel_3536
GAAGATCCAACGGAGCCACCAAGACTCAAGATTAATAAGAAAATTCCCTGGGGACCACCTTCTCCTCCTGCACCTGTCAT
GCATTCTCCCAGCAGAAAGGTGACTGTAAAGGAACAAGAGTGCAAGATTCCTCCTTGCATTTCAAACTGGAAAAATGCAA
AGGGTAATACAATTCCATTAGACAAACATCTCGCTGCTGATGGAAGAGGACTACAGACAGTACATATAAATTAAAATTTT
GCCAAACTGGCTGAAGCCCTCTATATTGCTAATTGGAAGGCTCGTGAAGCTGTGGAAATGTGTGCCCAAGTAGAGAGAAA
GATGGCTCAAAAATGAAAGGAGAAGCATGAAGAGAAACTTAGAGAAATGGCCCAAAAAGCCAGAGAGAGGAGAGCTGGAA
TCAAAACCCAGGTAGAAAAAGAGGATGGGGAGGCACGTGAGAGAGATGAAATCTGGCATGATAGGTGAAAAGAGAGACAG
AATGATAGGAATCCTTCCAGAGCAGCTCCTGATAAGAGGTCTAAACTCCAGAGAAATGAAAATCAGGATATCAGTGAAGT
CATTGCTCTTGGTGTGTCCAATCCGTGGGCTTTCAATGAAGTTCAATATGACCAGCGGTTTTTCAGCAAATCCAAGGGTA
TGAAGAGTGGATTTGCAGGTATATAAGATGAAATTCACAGTGTTTTTGATCAAGCCTGGAGAGGTGGTAAAGATATGGCC
CAGAGCATTTATAGGCCCAGTAAAAATGTGGACAAGGACGTGTATGATGATGACCTAGCAGCCAGAATAAAGACCAACAG
ATTTTTTTCCCAATTAAGAGTTTTCTGGTTTAGGCCATAGAGAAGACGAGAGGGAC

Alignment

ORF - retro_tbel_3536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.93 %
• Parental protein coverage: 53.36 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDPMEPPRFKINKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGR
          .DP.EPPR.KINKKIP.GPPSPPAPVMHSPSRK.TVKEQ.E.KIPPCISNWKNAKG.TIPLDK.LAADGR
Retrocopy EDPTEPPRLKINKKIPWGPPSPPAPVMHSPSRKVTVKEQ-ECKIPPCISNWKNAKGNTIPLDKHLAADGR

Parental  GLQTVHINENFAKLAEALYIADRKAREAVEMRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVE
          GLQTVHIN.NFAKLAEALYIA..KAREAVEM.AQVERKMAQK.KEKHEEKLREMAQKARERRAGIKT.VE
Retrocopy GLQTVHIN*NFAKLAEALYIANWKAREAVEMCAQVERKMAQK*KEKHEEKLREMAQKARERRAGIKTQVE

Parental  KEDGEARERDEIRHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQRLFN
          KEDGEARERDEI.HDR.KERQ.DRN.SRAAPDKRSKLQRNEN.DISEVIALGV.NP...NEVQYDQR.F.
Retrocopy KEDGEARERDEIWHDR*KERQNDRNPSRAAPDKRSKLQRNENQDISEVIALGVSNPWAFNEVQYDQRFFS

Parental  QTKGMDSGFAGGEDEIYNVYDQAWRGGKDMAQSIYRPSKNLDKDMYGDDLEARIKTNR-FVPDKEFSGSD
          ..KGM.SGFAG..DEI..V.DQAWRGGKDMAQSIYRPSKN.DKD.Y.DDL.ARIKTNR.F.P..EFSG..
Retrocopy KSKGMKSGFAGI*DEIHSVFDQAWRGGKDMAQSIYRPSKNVDKDVYDDDLAARIKTNR>FFPN*EFSGLG

Parental  RRQRGRE
          .R...R.
Retrocopy HREDERD

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_3536 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3536 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 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003976	2 retrocopies	retro_amel_163, retro_amel_912,
Canis familiaris	ENSCAFG00000030409	1 retrocopy	retro_cfam_195,
Felis catus	ENSFCAG00000001637	1 retrocopy	retro_fcat_635,
Loxodonta africana	ENSLAFG00000003482	2 retrocopies	retro_lafr_474, retro_lafr_787,
Myotis lucifugus	ENSMLUG00000005228	2 retrocopies	retro_mluc_387, retro_mluc_805,
Monodelphis domestica	ENSMODG00000005252	1 retrocopy	retro_mdom_1841,
Mustela putorius furo	ENSMPUG00000008724	1 retrocopy	retro_mputfur_551,
Mus musculus	ENSMUSG00000021039	2 retrocopies	retro_mmus_1022, retro_mmus_387,
Otolemur garnettii	ENSOGAG00000029825	1 retrocopy	retro_ogar_1404,
Sorex araneus	ENSSARG00000002279	3 retrocopies	retro_sara_403, retro_sara_568, retro_sara_727,
Tupaia belangeri	ENSTBEG00000014074	3 retrocopies	retro_tbel_2575, retro_tbel_2927, retro_tbel_3536 ,
Taeniopygia guttata	ENSTGUG00000012340	2 retrocopies	retro_tgut_15, retro_tgut_30,