RetrogeneDB ID: retro_tsyr_179

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_4582:36163..36977(+)
• Located in intron of: ENSTSYG00000004997

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSTSYG00000006259
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 1 [Source:HGNC Symbol;Acc:1488]

Sequence

>retro_tsyr_179
GAGGAGAAGGTACTTACCGCTGCTAAATTCATCACTCATGCACCTCCAGGGGAATTTAATGAAGTATTCGATGATGTTCA
GCTACTGTTTAGTAATGACAATCTCCTCAGGGAAGGGGCAGCACATGCATTTGTCCAGTATAAAATGGATCAGTTCATGC
CCGTGAAGCTAGAAGGAAATAAAGATCAGGTCCTAATTACAGAGCACAGTGACTTGGGTAGTAGCAGATTTTTAGATCCA
AGAAACAAAATTTTCTTTAAATTTGATCACTTATGGAAAGAAGCAGGTGATCCCCTAGTCAGAGGACATAGTAGGAGGCC
TGAGATCTTGGCAAGAATCCTTTGACAGTACTTTAAGGGCCTACATGAAAGATCATTATTCCAATGGCTTCAGTAATGTT
TATGCTAAAACTATAGATGGACAGCAGACTATTATTGCATGTATTGAAAGTCACCAATTTCAGCCTAAAAACTTCTGGAA
TGGTTGTTGGAGATCAGAGTGGAAGTTCACCATCACACCACATACAGCCCAGGTGGCTGGAGTGCTTAAGATTCAGGTTC
ACTATTATGAAGTTGGCAGTGTTCAGTTGGCCAGTTATAAGGATGTACAGGATTCAATTACTGTATCCAATGAAGTCCAA
ACTGCCAAGGAGTTTATTAAAATCACAGAGAATGCAGAAAATGAGTGTCAGACAGCAATTTGTGAAAACTATCAAACGAT
GTCAGATACCACATTCAAGGCCTTGTGCCGGCAGCTTCCAGTTACCCGCATGAAAATCGGATGGACCAAGATCCTCAGCT
ACAAGACTGACAAA

Alignment

ORF - retro_tsyr_179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.19 %
• Parental protein coverage: 96.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKLEGYEDQVLITEHG
          EEKV..AAKFITHAPPGEFNEVF.DV.LL..NDNLLREGAAHAF.QY.MDQF.PVKLEG..DQVLITEH.
Retrocopy EEKVLTAAKFITHAPPGEFNEVFDDVQLLFSNDNLLREGAAHAFVQYKMDQFMPVKLEGNKDQVLITEHS

Parental  DLGNSRFLDPRNKISFKFDHLRKEASDPQ-PEDVEGGLRSWRESCDSALRAYVKDHYSNGFCTVYAKTID
          DLG.SRFLDPRNKI.FKFDHL.KEA.DP...ED..GGLRSW.ES.DS.LRAY.KDHYSNGF..VYAKTID
Retrocopy DLGSSRFLDPRNKIFFKFDHLWKEAGDPL>SEDIVGGLRSWQESFDSTLRAYMKDHYSNGFSNVYAKTID

Parental  GQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSITVS
          GQQTIIACIESHQFQPKNFWNG.WRSEWKFTITP.TAQV.GVLKIQVHYYE.G.VQL.S.KDVQDSITVS
Retrocopy GQQTIIACIESHQFQPKNFWNGCWRSEWKFTITPHTAQVAGVLKIQVHYYEVGSVQLASYKDVQDSITVS

Parental  NEVQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGK
          NEVQTAKEFIKI.ENAENE.QTAI.ENYQTMSDTTFKAL.RQLPVTR.KI.W.KILSYK..K
Retrocopy NEVQTAKEFIKITENAENECQTAICENYQTMSDTTFKALCRQLPVTRMKIGWTKILSYKTDK

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_179 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 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Myotis lucifugus	ENSMLUG00000009796	1 retrocopy	retro_mluc_2483,
Mustela putorius furo	ENSMPUG00000004977	1 retrocopy	retro_mputfur_616,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Sorex araneus	ENSSARG00000001278	1 retrocopy	retro_sara_166,
Ictidomys tridecemlineatus	ENSSTOG00000015956	1 retrocopy	retro_itri_1044,
Tarsius syrichta	ENSTSYG00000006259	2 retrocopies	retro_tsyr_179 , retro_tsyr_471,
Vicugna pacos	ENSVPAG00000005361	1 retrocopy	retro_vpac_579,