RetrogeneDB ID: retro_tsyr_1866

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_62818:6182..6927(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PACRGL
• Ensembl ID: ENSTSYG00000001584
• Aliases: None
• Description: PARK2 co-regulated-like [Source:HGNC Symbol;Acc:28442]

Sequence

>retro_tsyr_1866
ATGCAGAAAACAGAGTGCTCTGGAGCTACACAGTTGAGAAACAGAGCCACAGGTAACTATGATCGAAGGACATCCTCATG
CACACAGATAAAGCATAGGACTTCAGTTCAGCGAAGCAAATCCTCATCGTCAGCCAGTTCTCCAGAGTCTGCAAGAAAAC
TTCATCCTCGACCAAGTGATAAACTTAACCCCATAAACAATTAACCCATTTGATGAACACTCAGCAGTCCCTTCTGCATT
TGCAGCTATTTACTCCAAAGGAGGTATTCCTTGCTGATTGATACATGGTTCAGTAAAACACAGATTACAGTGGGACTGTC
CTCCTGAAAATCTTTCATTTGATCCTCTTCTTGTTACTTTAGCTAAGGGTCTGAGAGAGACTAAACATCCACACACCTTT
GTGTCAAAAGAGGGTTTCAGAGAATTGCTTTTGGTTTATGGTGCTCCTGAAAAGGCTGTTCCTTTGCTCCCTAGACTGAT
TCCTGTGCTAAAGGCAACTCTGGTGCATTCAGATGATGCAGTATTTGAAAGAGGATTGAAAGCCTTGGTTCAGTTAAGTG
TTGTTGTTGGTCCTTATCTAAACGACCATCTGAAACATCTGCTTACAAGTCTTTCCAAGAGACTAATGGACAAGAAATTT
AAAGAGCCAATCACCAGTGCATTACAAAAGCTTCAGCAGCATGGTGGAAGTGGAAGTCTTTTCATCATCAAATCTAAAAT
CCCAACATATTGCTCCATATGCTGT

Alignment

ORF - retro_tsyr_1866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQKTECSGGTQLRNRVTGNYDRRTLSSTQIKHRTTVQQSKSSSSTCSPESVRKLHPRPSDKLNPR-TINP
          MQKTECSG.TQLRNR.TGNYDRRT.S.TQIKHRT.VQ.SKSSSS..SPES.RKLHPRPSDKLNP..TINP
Retrocopy MQKTECSGATQLRNRATGNYDRRTSSCTQIKHRTSVQRSKSSSSASSPESARKLHPRPSDKLNPI>TINP

Parental  FGEQSRAPSAFAAIYSKGGIPCRLVHGSVKHRLQWDCPPENLSFDPLLITLAEGLRETKHPYTFVS-EGF
          F.E.S..PSAFAAIYSKGGIPC.L.HGSVKHRLQWDCPPENLSFDPLL.TLA.GLRETKHP.TFVS.EGF
Retrocopy FDEHSAVPSAFAAIYSKGGIPC*LIHGSVKHRLQWDCPPENLSFDPLLVTLAKGLRETKHPHTFVSKEGF

Parental  RELLLVNGAPEKAVPLLPRLIPVVKATLVHSDDEVFERGLNALVQLSVVVGPYLNDHLKHLLTSLSKRLM
          RELLLV.GAPEKAVPLLPRLIPV.KATLVHSDD.VFERGL.ALVQLSVVVGPYLNDHLKHLLTSLSKRLM
Retrocopy RELLLVYGAPEKAVPLLPRLIPVLKATLVHSDDAVFERGLKALVQLSVVVGPYLNDHLKHLLTSLSKRLM

Parental  DKKFKEPITSALQKLEQHGGSGSLFIIKSKIPTYCSICC
          DKKFKEPITSALQKL.QHGGSGSLFIIKSKIPTYCSICC
Retrocopy DKKFKEPITSALQKLQQHGGSGSLFIIKSKIPTYCSICC

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_1866 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015625	1 retrocopy	retro_dord_96,
Homo sapiens	ENSG00000163138	1 retrocopy	retro_hsap_488,
Gorilla gorilla	ENSGGOG00000012603	1 retrocopy	retro_ggor_458,
Macropus eugenii	ENSMEUG00000009937	2 retrocopies	retro_meug_1836, retro_meug_1954,
Monodelphis domestica	ENSMODG00000000641	2 retrocopies	retro_mdom_1541, retro_mdom_1646,
Oryctolagus cuniculus	ENSOCUG00000002186	1 retrocopy	retro_ocun_258,
Pan troglodytes	ENSPTRG00000015945	1 retrocopy	retro_ptro_368,
Rattus norvegicus	ENSRNOG00000004140	1 retrocopy	retro_rnor_1543,
Tarsius syrichta	ENSTSYG00000001584	1 retrocopy	retro_tsyr_1866 ,