RetrogeneDB ID: retro_tsyr_273

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_683:42002..42951(-)
• Located in intron of: ENSTSYG00000014160

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTSYG00000004229
• Aliases: None
• Description: None

Sequence

>retro_tsyr_273
ATGAACCCCAGCACCCCCAGCTACCCCATGGCCTCTCTCTACGTGGGGGACCTGCACGCCGACGTGACCGAGGAGATGCT
CTACGAGAAGTTCAGCCCGGCCGGGCCCATCCTCTCCATCCGGGTCTGCAGGGACATGATCACCCACTGCTCCTTGGGCT
ACGCGTATGTGAACTTCCAGCAGCCGGCGGAGGCGCAGCGTGCTTTGGACACCATGAATTTTGATGTTATAAAGGGCAAG
CCAGTACACATCATGTAGTCTCAGCATGATCCATCACTTCGCAAAAATGGAGTAGGCAACATATTCGTTAAAAACCTGGA
CAAATCCATCGATAATAAGGCACTGTATGATACATTTTCTGCTTTTGGTAACATTCTTTCATGTAAGGTGGTTTGTGATG
AAAATGGTTCTAAGGGCTATGGATTTGTACACTTTGAAACACAGGAAGCAGCTGAAAGAGCTATTGAAAAAATGAACGGG
ATGCTCCTAAATGATCGTAAAGTATTTGTTGGACGATTTAAGTCTCGTAAAGAACGGGAAGCTGAGCTTGGAGCTAGGGC
AAAAGAGTTCACCAATGTTTACATCAAGAATTTTGGAGAAGACATGGATGATGAGCGCCTGAAGGATCTCTTTGGCAAGT
CTGGACCTGCCTTAAGCGTTAAAGTAATGACTGATGAAGTGGGAAATCCAAAGGATGTGGATTCGTAAGCTTTGAAAGGC
ATGAAGATGCACAGAAAGCTGTGGATGAGATGAATGGAAAGGAGCTCAATGGAAAACAGATTTATGTCGGCCGAGCTCAG
AAAAAAGTGGAACGGCAGACGGAATTCAAGCGCAAATTTGAGCAGATGAAGCAAGATAGGATCACCAGATACCAGGGTGT
TAACCTTCATGTGAAAAATCTTGATGATGAACGTCTCCGGATAGAGTTTCTCCGTTTGGTACAATAACT

Alignment

ORF - retro_tsyr_273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.71 %
• Parental protein coverage: 50.55 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNSSAPCYPMASLYVGDLHPDLIVTMLYEKFTPSGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD
          MN.S.P.YPMASLYVGDLH.D....MLYEKF.P.GPILSIRVCRDMIT..SLGYAYVNFQQPA.A.RALD
Retrocopy MNPSTPSYPMASLYVGDLHADVTEEMLYEKFSPAGPILSIRVCRDMITHCSLGYAYVNFQQPAEAQRALD

Parental  TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          TMNFDVIKGKPV.IM.SQ.DPSLRK.GVGNIF.KNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
Retrocopy TMNFDVIKGKPVHIM*SQHDPSLRKNGVGNIFVKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY

Parental  GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDL
          GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDL
Retrocopy GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDL

Parental  FGKFGPALSVKVMTDE-SGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRK
          FGK.GPALSVKVMTDE.SGKSKG.GFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTE.KRK
Retrocopy FGKSGPALSVKVMTDE<SGKSKGCGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTEFKRK

Parental  FEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEF-SPFGTIT
          FEQMKQDRITRYQGVNL.VKNLDD....ERLR.EF.SPFGTIT
Retrocopy FEQMKQDRITRYQGVNLHVKNLDD----ERLRIEF<SPFGTIT

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_273 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 17 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000348	1 retrocopy	retro_amel_1650,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus	ENSCPOG00000012917	1 retrocopy	retro_cpor_1324,
Dasypus novemcinctus	ENSDNOG00000008718	2 retrocopies	retro_dnov_1530, retro_dnov_2259,
Felis catus	ENSFCAG00000001874	1 retrocopy	retro_fcat_1927,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Gorilla gorilla	ENSGGOG00000006785	1 retrocopy	retro_ggor_1986,
Myotis lucifugus	ENSMLUG00000012245	1 retrocopy	retro_mluc_579,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Tarsius syrichta	ENSTSYG00000004229	2 retrocopies	retro_tsyr_1743, retro_tsyr_273 ,