RetrogeneDB ID: retro_tsyr_403

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_110598:5431..5914(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB2
• Ensembl ID: ENSTSYG00000005648
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 2 [Source:HGNC Symbol;Acc:9539]

Sequence

>retro_tsyr_403
CTCATCGGTCTCCAAGGCCCCGATTATGTCCTTGTCGCCTCCGACCGAGTGGCCACCGGCAATGTTGTCCAGATGAAGGA
TGATCATGATGAGATGCTTAAGATGAGAGAAAAAATCTTACTCCTATGTGTTGGAGAGGCTGGAGACACTGTACAGTTTG
CACAATATATTCAGAAAAATGTCCGACTTTATAAGATGCGAAATGGATATGAATTGTCTCCCACAGCAGCAGCTAATTTC
ACATGCTGAAACCCGACTGATTGTCTTTGGGGTCGGACCCCATATCATGTGAACCTCTTCCTGGCTGGCTACGATGAGCA
TAAGGGACCAGCGCTCCACCACATGGACTACCTAGCAGCCTTGACCGAGGCTCCTTTTGCAGCCCAAGGCTATGGTACCT
TCCTGACTCTCAGTAACGGATACCACACAACTACTATCTCACAGGAGAGGGCAGCAGAGCTTCTTAAGAAATGTCTAGAG
GAG

Alignment

ORF - retro_tsyr_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.37 %
• Parental protein coverage: 65.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNGY
          LIG.QGPDYVLVASDRVA..N.VQMKDDHD.M.KM.EKILLLCVGEAGDTVQFA.YIQKNV.LYKMRNGY
Retrocopy LIGLQGPDYVLVASDRVATGNVVQMKDDHDEMLKMREKILLLCVGEAGDTVQFAQYIQKNVRLYKMRNGY

Parental  ELSPTAAANFTRRNLADCLRSRTPYHVNLLLAGYDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSIL
          ELSPTAAANFT..N..DCL..RTPYHVNL.LAGYDEH.GPAL..MDYLAAL..APFAA.GYG.FLTLS..
Retrocopy ELSPTAAANFTC*NPTDCLWGRTPYHVNLFLAGYDEHKGPALHHMDYLAALTEAPFAAQGYGTFLTLS--

Parental  DRYYTPTISRERAVELLRKCLEE
          ..Y.T.TIS.ERA.ELL.KCLEE
Retrocopy NGYHTTTISQERAAELLKKCLEE

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_403 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000715	1 retrocopy	retro_amel_743,
Canis familiaris	ENSCAFG00000003543	1 retrocopy	retro_cfam_1291,
Callithrix jacchus	ENSCJAG00000001547	1 retrocopy	retro_cjac_2110,
Dasypus novemcinctus	ENSDNOG00000017663	1 retrocopy	retro_dnov_159,
Equus caballus	ENSECAG00000021615	1 retrocopy	retro_ecab_769,
Echinops telfairi	ENSETEG00000019511	1 retrocopy	retro_etel_1529,
Felis catus	ENSFCAG00000030845	1 retrocopy	retro_fcat_1803,
Macropus eugenii	ENSMEUG00000000421	1 retrocopy	retro_meug_1235,
Monodelphis domestica	ENSMODG00000017902	1 retrocopy	retro_mdom_79,
Mustela putorius furo	ENSMPUG00000014891	1 retrocopy	retro_mputfur_1550,
Ochotona princeps	ENSOPRG00000012259	2 retrocopies	retro_opri_76, retro_opri_762,
Pteropus vampyrus	ENSPVAG00000001871	1 retrocopy	retro_pvam_909,
Sorex araneus	ENSSARG00000000409	2 retrocopies	retro_sara_557, retro_sara_660,
Sarcophilus harrisii	ENSSHAG00000016996	1 retrocopy	retro_shar_794,
Tupaia belangeri	ENSTBEG00000005230	1 retrocopy	retro_tbel_4039,
Tarsius syrichta	ENSTSYG00000005648	2 retrocopies	retro_tsyr_403 , retro_tsyr_912,