RetrogeneDB ID: retro_tsyr_2044

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_82782:4543..5360(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPHLN1
• Ensembl ID: ENSTSYG00000010740
• Aliases: None
• Description: periphilin 1 [Source:HGNC Symbol;Acc:19369]

Sequence

>retro_tsyr_2044
AGAGAACAAGTACCTCCTCAAAGTCACCCCAGTGATGAATCTGGTTATAGATGGACAAGAGATGATCATTCTGCAAGCCG
ACAACCTGAATACAGGGACGTGAGAGATGGTTTTAGAAGAAAAAGTTTCTACTCTTCCCATTACGTGAGAGACCGGTCTC
CTCATAAAAGCGACGCTCCTTTTTTTCAGAGAATCACCTGTTGGCCGAAAGAATTCTCCACACAGTAGATCTGGCTCCAG
TGTCAGTAGTAGAAGCTACTCTCCAGAAAGAAGCAAAACATACTCTTTCCATCAATCTCAACATAGAAAGTCCGTGCATC
CTGGTGCCTTCTTCTACAAACGACAGAATGAAGGAAAGCCAGAAAGAGGTAGAGACCTGTCCAGTCTTTGAAAACATCAA
GAGGCACTTAACCCTCAAGTTCTTCAGCAGTTCCTTCATCAGAGGTGTTAGACAAACCCAGTAGGCTCAGTGAAAAGGAA
CTTGTTGAGGCTGCAAACAAGTGGGCTGCTGAAAACTAGAGAAGTCAGATGAGAGTAGCTTGCCTGAAATTTCCGAGTTT
GAGACTGGATCCACAGCACCGTTGTTCATTGACTAGCCAGAAGAACCCCAGTCAAATGCAACAGATGGCACAGAATTACT
TGAAGACAGCCAGCTAACCAGTCGCTCTAAAGCAATAGCATCAAAACCAAAGAGATCGAAGATGTTTACAGACAAGACTG
TGAAACTTTTGGGATGGTGGTGAAAATGCTGATTGAAAAAGATCCTTCATTAGAAAAGTCTATACAGTTTGCCTTTAGGC
AGAATTTACATGAAATA

Alignment

ORF - retro_tsyr_2044 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.61 %
• Parental protein coverage: 79.35 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RRSGPP--HRGDESGYRWTRDDHSASRQPEYRDVRDGFRRKSFYSSHYVRDRSPHKRDAPFF-RESPVGR
          R...PP..H..DESGYRWTRDDHSASRQPEYRDVRDGFRRKSFYSSHYVRDRSPHK.DAPFF.RESPVGR
Retrocopy REQVPPQSHPSDESGYRWTRDDHSASRQPEYRDVRDGFRRKSFYSSHYVRDRSPHKSDAPFF>RESPVGR

Parental  KDSPHSRSGSSVSSRSYSPERSKTYSFHQSQHRKSVHPGAFFYKRQN-EGKPERGKERPVQSLKTSRDTS
          K.SPHSRSGSSVSSRSYSPERSKTYSFHQSQHRKSVHPGA.F......E....R...RPVQSLKTSR.T.
Retrocopy KNSPHSRSGSSVSSRSYSPERSKTYSFHQSQHRKSVHPGA-FFYKRQ<E*RKARKR*RPVQSLKTSRGT*

Parental  PSSSSAVPSSK---KPSRLSEKELVEAASKWAAE-KLEKSDESNLPEISEFETGSTAPLFIDQPEEPESN
          PSSSSAVPSS....KPSRLSEKELVEAA.KWAAE.KLEKSDES.LPEISEFETGSTAPLFID.PEEP.SN
Retrocopy PSSSSAVPSSEVLDKPSRLSEKELVEAANKWAAE<KLEKSDESSLPEISEFETGSTAPLFID*PEEPQSN

Parental  ATDGIELFEDSQLTSRSKAIAS-KTKEIEEVYRQDCETFGMVVKMLIEKDPSLEKSIQFALRQNLHEI
          ATDG.EL.EDSQLTSRSKAIAS.KTKEIE.VYRQDCETFGMVVKMLIEKDPSLEKSIQFA.RQNLHEI
Retrocopy ATDGTELLEDSQLTSRSKAIAS<KTKEIEDVYRQDCETFGMVVKMLIEKDPSLEKSIQFAFRQNLHEI

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_2044 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.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010693	1 retrocopy	retro_chof_1231,
Callithrix jacchus	ENSCJAG00000017726	1 retrocopy	retro_cjac_1547,
Cavia porcellus	ENSCPOG00000012266	2 retrocopies	retro_cpor_744, retro_cpor_745,
Dasypus novemcinctus	ENSDNOG00000002007	1 retrocopy	retro_dnov_1790,
Equus caballus	ENSECAG00000016067	1 retrocopy	retro_ecab_209,
Mus musculus	ENSMUSG00000036167	3 retrocopies	retro_mmus_1657, retro_mmus_3561, retro_mmus_79,
Otolemur garnettii	ENSOGAG00000004012	2 retrocopies	retro_ogar_1387, retro_ogar_2103,
Tarsius syrichta	ENSTSYG00000010740	1 retrocopy	retro_tsyr_2044 ,