RetrogeneDB ID: retro_tsyr_148

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_3867:7785..8794(+)
• Located in intron of: ENSTSYG00000007576

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSPT1
• Ensembl ID: ENSTSYG00000013812
• Aliases: None
• Description: G1 to S phase transition 1 [Source:HGNC Symbol;Acc:4621]

Sequence

>retro_tsyr_148
CGAGGCGAAACACCTGTGGAATACTCTCAGGAGGAACAGTCATTGCTGTGTGAGGGTTCAAATTCAGCTGTTAGCATGGA
ACTTTCAGAACCTGTTGTAGAAAATGGAGAAACGGAAATGTCCCCAGAAGAATCATGGGAGCACAAAGAAGAAATAAGTG
AAGCAGAGCGAGGGGGTGGTTCCTTGGGAGATGGAAGACCACCAGAGGAAAGTGCCCAAGAAATGATGGAGGAGAAAGAG
GAGATACCAAATCCTAAATCTGTGGTTGCACCTACAGGTGCTCCTCAAAAGGAGCATGTAAATGTAGTGTTCATTGGCCA
TGTGGATGCTGGCAAGTCAACCATTGAAGGACAAATCATGTATTTGACTGGAATGGCTGACAGAAGGACACTTGAGAAGT
ATGAAAGAGAAGCTAAAGAAAAAAAACAGAGAAACTTGGTACTTGTTTTGGGCCTTAGACACAAATCAGGAAGAATGAGA
CAAGGGTAAAACAGTAGAAGTGGGTCGTGCCTATTTTGAAACTGAAAAGAAGCATTTCATAATTCTGGATGCCCCTGGAC
ACAAGAGTTTTGTCCCAAATTTGATTGGTGGTACCTCCCAAGCTGATTTGGCTGTGCTGGTCATTTCAGCCAGGAAAGGG
GAATTCAAAACTGGGTTTGAAAAAGGAGGACAGACAAGAGAACATGCAATGTTGGCAAAGACAGCAGGTGTAAAACACTT
AATTGTGCTTATTAATAAGATGGATGACCCAACAGTAAATTGGAGTAATGAGAGGTATGAAGAACGTAAAGAGAAACTAG
TGCCATTTTTTTAAAAAGTGGGCTTCCTTCCCAAAAAGGACATTCATTTTATGCCCTGCTCAGGACTGACTGGAGCGAAT
CTCAAAGAGCAATCAGATTTCTGTCCTTGGTACATTGGATTACCATTTATTCCATATCTGGATAATTTGCCAAACTTCAA
TAGATCAGTTGATGGACCAATCAGGCTGCCAATTGTGGATAAGTACAAG

Alignment

ORF - retro_tsyr_148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.69 %
• Parental protein coverage: 63.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKSSPVESSQEDQSLLCEGSNSAVSMELSEPVVENGETEMSPEESWEHKEEISEAEPGGGSLGDGRPPEE
          R...PVE.SQE.QSLLCEGSNSAVSMELSEPVVENGETEMSPEESWEHKEEISEAE.GGGSLGDGRPPEE
Retrocopy RGETPVEYSQEEQSLLCEGSNSAVSMELSEPVVENGETEMSPEESWEHKEEISEAERGGGSLGDGRPPEE

Parental  SAQEMMEEEEEIPKPKSVVAPPGAPKKEHVNVVFIGHVDAGKSTIGGQIMYLTGMVDKRTLEKYEREAKE
          SAQEMMEE.EEIP.PKSVVAP.GAP.KEHVNVVFIGHVDAGKSTI.GQIMYLTGM.D.RTLEKYEREAK.
Retrocopy SAQEMMEEKEEIPNPKSVVAPTGAPQKEHVNVVFIGHVDAGKSTIEGQIMYLTGMADRRTLEKYEREAKX

Parental  KN-RETWYLSWALDTNQEERDKGKTVEVGRAYFETEKKHFTILDAPGHKSFVPNMIGGASQADLAVLVIS
          ...RETWYL.WALDTNQEE.DKGKTVEVGRAYFETEKKHF.ILDAPGHKSFVPN.IGG.SQADLAVLVIS
Retrocopy XX>RETWYLFWALDTNQEE*DKGKTVEVGRAYFETEKKHFIILDAPGHKSFVPNLIGGTSQADLAVLVIS

Parental  ARKGEFETGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEECKEKLVPFLKKVGFNPKK
          ARKGEF.TGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEE.KEKLVPF..KVGF.PKK
Retrocopy ARKGEFKTGFEKGGQTREHAMLAKTAGVKHLIVLINKMDDPTVNWSNERYEERKEKLVPFF*KVGFLPKK

Parental  DIHFMPCS-LTGANLKEQSDFCPWYIGLPFIPYLDNLPNFNRSVDGPIRLPIVDKYK
          DIHFMPCS.LTGANLKEQSDFCPWYIGLPFIPYLDNLPNFNRSVDGPIRLPIVDKYK
Retrocopy DIHFMPCSGLTGANLKEQSDFCPWYIGLPFIPYLDNLPNFNRSVDGPIRLPIVDKYK

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_148 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 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,