RetrogeneDB ID: retro_tbel_3810

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_16416:5253..6143(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000010713
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GSPT1
• Ensembl ID: ENSTBEG00000008873
• Aliases: None
• Description: G1 to S phase transition 1 [Source:HGNC Symbol;Acc:4621]

Sequence

>retro_tbel_3810
CCTGTGGAACCTCCCAAAGAGGAACCCTTAGTGTGGGAAGGTTCCAATTCAGCCGTTACCATGGAACTTTCAGAACCTGT
TGTAGAGAATGGAGAGGTGGAAATGATCCTAGAAGAATCATGGGAGCACAGTAAAGAAGTAAGTGAAGCAGAGCCTGGGG
GTGATTCCTTGGGAGATTCAGGGCCTCCAGAAGAAAGTGGCCAGGAATGATGGAGGAAAAAGAGACATGAGAAATCAAAT
CTGTGGTCGTGCCTTCGGTGCTCTAAAAAGGAACATGTAATGTGGTCTTCATCGGGCATGTTGATGCTGGCAAGTCAACC
ATCGGAGGACAAATAATGTTTTTGACCGGAATGGTTGACAAAAGGACTCTTGAGAAATATGAAAGAGAAGCCAAGGAAAA
AAACAGAGAAACCTGGTATTTGTCCTGGGCCTTAGATACAAATCAGGAAGAACGAGACAAGGGTAAAACAGTAGAAGTGG
GTCGTGCTTATTTTGAAACAGAAAAGAAACACTTCACAATTTTAGATGCTCCTGGCCACAAGAGTTTTGTCCCAAATATG
ATTGGTGGTGCTTCTCAAGCTGATTTGGCTGTGCTGGTCATCTCTGCCAGGAAAGGGGAGTTTGAAACTGGATTCGAAAA
AGGTGGACAGACAAGAGAACATGCAATGTTAGCAAAAACAGCGGGGGTAAAACATTTAATAGTGCTTATTAATAAAATGG
ATGATCCCACAGTAAATTGGAGCAGCGAGAGATATGAAGAATGTAAAGAAAAATTGGTGCCCTTTTTGAAAAAAGTTGGC
TTCAGTCCAAAAAAGGACATTTACTTTATGCCCTGCTCAGGACTGACAGGAGCAAATATTAAGGAGCAATCAGATTTCTG
TCCTTGGTAC

Alignment

ORF - retro_tbel_3810 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.49 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PVESSQDEQSLLCEGSNSAVSMELSEPVVENGETEMSPEESWEHKDEISEAEPGGGSLGDGRPPEESAQE
          PVE....E..L..EGSNSAV.MELSEPVVENGE.EM..EESWEH..E.SEAEPGG.SLGD...P.E....
Retrocopy PVEPPKEEP-LVWEGSNSAVTMELSEPVVENGEVEMILEESWEHSKEVSEAEPGGDSLGDSG-PPEESGQ

Parental  M-MEEEEELPKPKSVVAPPGA-PKKEHV-NVVFIGHVDAGKSTIGGQIMYLTGMVDTRTLEKYAREAKEK
          ..M.EE.E....KS.V..P....KKEHV.NVVFIGHVDAGKSTIGGQIM.LTGMVD.RTLEKY.REAKEK
Retrocopy E<MMEEKET*EIKS-VVVPSV>SKKEHV<NVVFIGHVDAGKSTIGGQIMFLTGMVDKRTLEKYEREAKEK

Parental  NRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISAR
          NRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISAR
Retrocopy NRETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVISAR

Parental  KGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEECKEKLVPFLKKVGFNPKKDI
          KGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWS.ERYEECKEKLVPFLKKVGF.PKKDI
Retrocopy KGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSSERYEECKEKLVPFLKKVGFSPKKDI

Parental  HFMPCSGLTGANLKEQSDFCPWY
          .FMPCSGLTGAN.KEQSDFCPWY
Retrocopy YFMPCSGLTGANIKEQSDFCPWY

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_3810 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3810 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 25 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009589	1 retrocopy	retro_amel_4,
Bos taurus	ENSBTAG00000003577	2 retrocopies	retro_btau_1793, retro_btau_1840,
Canis familiaris	ENSCAFG00000018856	1 retrocopy	retro_cfam_2072,
Callithrix jacchus	ENSCJAG00000018191	1 retrocopy	retro_cjac_618,
Cavia porcellus	ENSCPOG00000009381	1 retrocopy	retro_cpor_73,
Equus caballus	ENSECAG00000021195	1 retrocopy	retro_ecab_739,
Echinops telfairi	ENSETEG00000018249	1 retrocopy	retro_etel_1626,
Felis catus	ENSFCAG00000022281	1 retrocopy	retro_fcat_1913,
Gorilla gorilla	ENSGGOG00000004071	1 retrocopy	retro_ggor_2906,
Microcebus murinus	ENSMICG00000014137	1 retrocopy	retro_mmur_28,
Myotis lucifugus	ENSMLUG00000000792	1 retrocopy	retro_mluc_98,
Macaca mulatta	ENSMMUG00000023178	1 retrocopy	retro_mmul_118,
Monodelphis domestica	ENSMODG00000004728	1 retrocopy	retro_mdom_1420,
Mustela putorius furo	ENSMPUG00000014504	1 retrocopy	retro_mputfur_147,
Mus musculus	ENSMUSG00000062203	1 retrocopy	retro_mmus_238,
Nomascus leucogenys	ENSNLEG00000010199	1 retrocopy	retro_nleu_2705,
Oryctolagus cuniculus	ENSOCUG00000004759	1 retrocopy	retro_ocun_1664,
Otolemur garnettii	ENSOGAG00000007083	1 retrocopy	retro_ogar_100,
Pteropus vampyrus	ENSPVAG00000005009	1 retrocopy	retro_pvam_1426,
Rattus norvegicus	ENSRNOG00000002335	1 retrocopy	retro_rnor_2931,
Sarcophilus harrisii	ENSSHAG00000005908	1 retrocopy	retro_shar_14,
Ictidomys tridecemlineatus	ENSSTOG00000015406	1 retrocopy	retro_itri_109,
Tupaia belangeri	ENSTBEG00000008873	2 retrocopies	retro_tbel_3810 , retro_tbel_4659,
Tarsius syrichta	ENSTSYG00000013812	2 retrocopies	retro_tsyr_1169, retro_tsyr_148,
Tursiops truncatus	ENSTTRG00000011630	1 retrocopy	retro_ttru_12,