RetrogeneDB ID: retro_tsyr_1218

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_35408:14171..14898(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRYZ
• Ensembl ID: ENSTSYG00000004193
• Aliases: None
• Description: crystallin, zeta (quinone reductase) [Source:HGNC Symbol;Acc:2419]

Sequence

>retro_tsyr_1218
ACAGGTGACAGGGTCTTCACGACCAGCACGCTCTCTGGGGGCTATGCGAAGTACACGCTTGCAGCGGATCACACCGTCTA
CAAACTGTCCGACGAGCTGGACTTCTGGTAAGACGTGGCCATCGGTGTCCCATATTTCACGGAGTTTTGAGCTCTGATCC
ACAGTGCCCACGCGAAGGCTGGCGAGAGCGTTCTGGTTCACGGGGCTAGCGGAGGAGTTGGCTTAGCAGCGTGCCAGATT
GCTAGAGTTTATGGCTTGAGAGTTTTGGGCACGGCTGGTACCGAGGAGGGACGGAAGATTGTCTTTCAAAATGGAGCCCA
TGAAGTGTTTAATCACCGAGAAGTTAATTACATTGATAAAATTAAGAAATCTGTTGGTGAGAGAGGAATTGATGTGACTA
TTGAAATGTTAGCGAATGTAAATCTTAGTAAAGATTTGACATATTCTGTCATATGGAGGAAGAGTCATAGTTGTTGGCAA
CAGAGGTACTACTGAAATCAAACCTCGGGATACTATGGCCAAGGAGTCTAGTATCATTGGAGTTCATCTCTGTTCCCCAA
CCAAGGAGGAATTTCAGCAGTTTGCAGCCGCCCTTCAAGCTGGAATGGAAATTGGTTGGTTGAAGCCTGTAATAGGTTCT
TGGTATCCGTTGGAGAAGGTGGCCCAAGCTCATGAAAATATCATTCACAGCAGTGGGGCTACTGGAAAAATGGTCCTTCT
CTTACGA

Alignment

ORF - retro_tsyr_1218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.3 %
• Parental protein coverage: 80.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGDRVFTTSTLSGGYAEYALAADHTVYKLPDELDFQQGAAIGIPYFTAFRALIHSARAKAGESVLVHGAS
          TGDRVFTTSTLSGGYA.Y.LAADHTVYKL.DELDF....AIG.PYFT.F.ALIHSA.AKAGESVLVHGAS
Retrocopy TGDRVFTTSTLSGGYAKYTLAADHTVYKLSDELDFW*DVAIGVPYFTEF*ALIHSAHAKAGESVLVHGAS

Parental  GGVGLAACQIARAYGLRVLGTAGTEEGRKVVLQNGAHEVFNHREVNYIDKIKKSVGERGIDVIIEMLANV
          GGVGLAACQIAR.YGLRVLGTAGTEEGRK.V.QNGAHEVFNHREVNYIDKIKKSVGERGIDV.IEMLANV
Retrocopy GGVGLAACQIARVYGLRVLGTAGTEEGRKIVFQNGAHEVFNHREVNYIDKIKKSVGERGIDVTIEMLANV

Parental  NLSKDL-NLLSYGGRVIVVGNRGTIEINPRDTMAKETSIIGVHLFSSTKEEFQQFAAALQAGMEIGWLKP
          NLSKDL...LSYGGRVIVVGNRGT.EI.PRDTMAKE.SIIGVHL.S.TKEEFQQFAAALQAGMEIGWLKP
Retrocopy NLSKDL>HILSYGGRVIVVGNRGTTEIKPRDTMAKESSIIGVHLCSPTKEEFQQFAAALQAGMEIGWLKP

Parental  VIGSRYPLEKVAQAHENIIHGGGATGKMVLLLR
          VIGS.YPLEKVAQAHENIIH..GATGKMVLLLR
Retrocopy VIGSWYPLEKVAQAHENIIHSSGATGKMVLLLR

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_1218 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 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003162	1 retrocopy	retro_btau_1433,
Canis familiaris	ENSCAFG00000020404	1 retrocopy	retro_cfam_870,
Choloepus hoffmanni	ENSCHOG00000005167	1 retrocopy	retro_chof_1772,
Felis catus	ENSFCAG00000030626	1 retrocopy	retro_fcat_1907,
Homo sapiens	ENSG00000116791	1 retrocopy	retro_hsap_3884,
Loxodonta africana	ENSLAFG00000011371	1 retrocopy	retro_lafr_527,
Macaca mulatta	ENSMMUG00000014593	2 retrocopies	retro_mmul_1026, retro_mmul_1728,
Mustela putorius furo	ENSMPUG00000010969	1 retrocopy	retro_mputfur_119,
Mus musculus	ENSMUSG00000028199	1 retrocopy	retro_mmus_1314,
Nomascus leucogenys	ENSNLEG00000009543	2 retrocopies	retro_nleu_1890, retro_nleu_3115,
Otolemur garnettii	ENSOGAG00000011586	1 retrocopy	retro_ogar_179,
Pongo abelii	ENSPPYG00000001235	2 retrocopies	retro_pabe_1909, retro_pabe_3165,
Pan troglodytes	ENSPTRG00000000865	1 retrocopy	retro_ptro_1598,
Tupaia belangeri	ENSTBEG00000016750	3 retrocopies	retro_tbel_1665, retro_tbel_2353, retro_tbel_3800,
Tarsius syrichta	ENSTSYG00000004193	2 retrocopies	retro_tsyr_1218 , retro_tsyr_1884,
Tursiops truncatus	ENSTTRG00000010471	2 retrocopies	retro_ttru_555, retro_ttru_958,