RetrogeneDB ID: retro_tsyr_1838

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_615781:3..796(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBBP7
• Ensembl ID: ENSTSYG00000002385
• Aliases: None
• Description: retinoblastoma binding protein 7 [Source:HGNC Symbol;Acc:9890]

Sequence

>retro_tsyr_1838
GAGTAGAACATATGGAAAAAGAACACCCCTTTTCTTTGTTGATGACCCATGCCTTTGGAGTGGCCCAGCCTAACTGCACA
GTGGCTTCCAGACATAACCAGACCAGAAGGGAAAGATTTCAGCATTTGTCAACTTGTCCTGGGGATACACACATTGGATG
AACAAAACCATCTTGTGATAGCCAGTGTGCAACTCCCTAATGATGATGCTCAGTTTGATGCGTCACACTACAACAAAGGA
AAAGGAGAATTTGGAAGTTTTGGTTCGGTTAGTGGAAAATTGAAATAGAAATCAATATCAACCATGACGGAAACGTAAAC
AGGGCTTGTTATATGCACCAGAACCCTTGTATCATTGCAACAAAGACTCCATCCTGCTGTGTTCTTGTTTTTGACTTTAT
AAAACATCCTTCTAAACCAGACCCTTCTGGAGAGTGCAACCCAGACTTATGTCTTTGTGTACATCAGAAGGAAGGCTATG
GGCTTTCTTGAAACCCAAATCTCAGTGGGCACTTACTTAGTGCTTCAGATGACCCATACCATCTGGCTATGGGATATCGG
TGCCATTCCAAAGGAAGGAAAAGTAGTGGATGCGAAGACCATGTTTACAGGACATACAGCAGTTGTTGAAGATTTTCCTG
GCATCTGTTCTGTGAGTCTCTGTTTGGGTCGTTGCTGATGATCAGAAGCTTATAATTTGGGGTACTCGTTCAAACAATAC
TTCTAAACCAAGCCACTCATTTGATGCTCACACTGCTGAAGTGAACTGCCTCTCTTTAACTCCTTATAGTGAG

Alignment

ORF - retro_tsyr_1838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.36 %
• Parental protein coverage: 56.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  EYKIWKKNT-PFLYDLVMTHA-LQWPSLTVQWLPEVTKPEGKDYALHWLVLGTHTSDEQNHLVVARVHIP
          E..IWKKNT.PF...L.MTHA.L.WPSLT.QWLP..T.PEGKD.....LVLG.HT.DEQNHLV.A.V..P
Retrocopy E*NIWKKNT<PF--SLLMTHA>LEWPSLTAQWLPDITRPEGKDFSICQLVLGIHTLDEQNHLVIASVQLP

Parental  NDDAQFDASHCDSDKGEFGGFGSVTGK-IECEIKINHEGEVNRARYMPQNPHIIATKTPSSDVLVFDYTK
          NDDAQFDASH....KGEFG.FGSV.GK.IE.EI.INH.G.VNRA.YM.QNP.IIATKTPS..VLVFD..K
Retrocopy NDDAQFDASHYNKGKGEFGSFGSVSGK<IEIEININHDGNVNRACYMHQNPCIIATKTPSCCVLVFDFIK

Parental  HPAKPDPSGECNPDLRLRGHQKEGYGLSWNSNLSGHLLSASDD-HTVCLWDINAGPKEGKIVDAKAIFTG
          HP.KPDPSGECNPDL.L..HQKEGYGLS.N.NLSGHLLSASDD.HT..LWDI.A.PKEGK.VDAK..FTG
Retrocopy HPSKPDPSGECNPDLCLCVHQKEGYGLS*NPNLSGHLLSASDD>HTIWLWDIGAIPKEGKVVDAKTMFTG

Parental  HSAVVED-VAWHLLHESLFGS-VADDQKLMIWDTRSNTTSKPSHLVDAHTAEVNCLSFNPYSE
          H.AVVED...WHL..ESLFGS.VADDQKL.IW.TRSN.TSKPSH..DAHTAEVNCLS..PYSE
Retrocopy HTAVVED<FSWHLFCESLFGS<VADDQKLIIWGTRSNNTSKPSHSFDAHTAEVNCLSLTPYSE

Legend:

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

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_1838 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002820	1 retrocopy	retro_btau_1579,
Mus musculus	ENSMUSG00000031353	1 retrocopy	retro_mmus_3529,
Oryctolagus cuniculus	ENSOCUG00000000683	1 retrocopy	retro_ocun_1939,
Otolemur garnettii	ENSOGAG00000014995	1 retrocopy	retro_ogar_2220,
Petromyzon marinus	ENSPMAG00000007189	1 retrocopy	retro_pmar_26,
Pan troglodytes	ENSPTRG00000021702	5 retrocopies	retro_ptro_1802, retro_ptro_1909, retro_ptro_2226, retro_ptro_2987, retro_ptro_896,
Rattus norvegicus	ENSRNOG00000005157	1 retrocopy	retro_rnor_1182,
Sorex araneus	ENSSARG00000008079	3 retrocopies	retro_sara_308, retro_sara_571, retro_sara_602,
Tupaia belangeri	ENSTBEG00000010151	2 retrocopies	retro_tbel_3031, retro_tbel_4341,
Tarsius syrichta	ENSTSYG00000002385	4 retrocopies	retro_tsyr_1608, retro_tsyr_1838 , retro_tsyr_1957, retro_tsyr_427,