RetrogeneDB ID: retro_tsyr_469

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_123296:4583..5149(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL7L1
• Ensembl ID: ENSTSYG00000004848
• Aliases: None
• Description: ribosomal protein L7-like 1 [Source:HGNC Symbol;Acc:21370]

Sequence

>retro_tsyr_469
AAGAGCAAAGAAAAAATCCCTTTGGTTCCAGAAAATCTTCTGAAAAATAGGAAGGTTTATCAAGTCCTCAAAGTCACCCA
GGCAAAGCAGGCATTTGGGCAAAGAAGGAGCAGAGGAAAGAAAAGGGTTCAGGTTTAAACAATTGATATCATTCTTACAC
AATTTCTGGTGGCAGAATTGTGACAATGTGCATCTCAGAAGACTAGAAATGAAACCTCATGCCTTGAAATTGCCAGATAA
ACATTCCTTTGATTCTATTGTTCACATCCAAAGGACTGATGGGGTGAGCTCTTGATGCAGAGGACATCCCAAGACTTTGC
CTGAAGAAAATTTTCAGCGGTGTCTTTGTCAAAGTCAACCCCCAGAACCTAAAAACGCTGCATATTGTGGAGCCTTATGC
AACCTGGAGATTTCCAAATTTGAAGTCTGTCCAGGAACTTATCTTAAGTAGACAAGTCAAAGTCTAGAATAAGACCATTC
TTCTGACAGATAACACAGTGATTGGGGAGTACCTGGGCAAGTTTAGTGTCATTTACTTGGAAGACTTCATTTATGAAATT
GCCTTC

Alignment

ORF - retro_tsyr_469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.72 %
• Parental protein coverage: 77.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EGQRKIPLVPENLLKKRKAYQALKATQAKQA-LLARKEQRKGKG-LKFKRLELFLYDSWRQKRDSVRLRR
          ....KIPLVPENLLK.RK.YQ.LK.TQAKQA...A.KEQRK.KG...FK.L..FL...W.Q..D.V.LRR
Retrocopy KSKEKIPLVPENLLKNRKVYQVLKVTQAKQA<IWAKKEQRKEKG<FRFKQLISFLHNFWWQNCDNVHLRR

Parental  LEVKPHALELPDKHSLAFVVRIQRIDGVSS-LVQRT-IARLHLKKIFSGVFVKVTPQRLKMLRIVETYVT
          LE.KPHAL.LPDKHS....V.IQR.DGVSS.L.QRT.I.RL.LKKIFSGVFVKV.PQ.LK.L.IVE.Y.T
Retrocopy LEMKPHALKLPDKHSFDSIVHIQRTDGVSS<LMQRT<IPRLCLKKIFSGVFVKVNPQNLKTLHIVEPYAT

Parental  CGFPNLKSVRELILKRGQARVKNKTIPLTDNTVIEEHLGKFGVICLEDLIHEIAF
          ..FPNLKSV.ELIL.R.Q..V.NKTI.LTDNTVI.E.LGKF.VI.LED.I.EIAF
Retrocopy WRFPNLKSVQELILSR-QVKV*NKTILLTDNTVIGEYLGKFSVIYLEDFIYEIAF

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_469 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 26 parental genes, and 107 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012791	2 retrocopies	retro_amel_1260, retro_amel_243,
Bos taurus	ENSBTAG00000018478	2 retrocopies	retro_btau_588, retro_btau_816,
Canis familiaris	ENSCAFG00000001728	4 retrocopies	retro_cfam_1180, retro_cfam_1464, retro_cfam_1638, retro_cfam_330,
Choloepus hoffmanni	ENSCHOG00000000306	4 retrocopies	retro_chof_1168, retro_chof_1404, retro_chof_388, retro_chof_478,
Cavia porcellus	ENSCPOG00000021189	2 retrocopies	retro_cpor_1134, retro_cpor_653,
Dasypus novemcinctus	ENSDNOG00000013485	1 retrocopy	retro_dnov_689,
Equus caballus	ENSECAG00000003113	1 retrocopy	retro_ecab_998,
Erinaceus europaeus	ENSEEUG00000010431	1 retrocopy	retro_eeur_90,
Echinops telfairi	ENSETEG00000002419	3 retrocopies	retro_etel_1151, retro_etel_1823, retro_etel_542,
Felis catus	ENSFCAG00000009707	1 retrocopy	retro_fcat_143,
Gorilla gorilla	ENSGGOG00000009958	15 retrocopies	retro_ggor_1009, retro_ggor_1013, retro_ggor_1253, retro_ggor_1261, retro_ggor_1904, retro_ggor_2099, retro_ggor_2108, retro_ggor_2113, retro_ggor_2162, retro_ggor_2282, retro_ggor_2457, retro_ggor_2524, retro_ggor_2591, retro_ggor_2659, retro_ggor_2973,
Macaca mulatta	ENSMMUG00000021313	1 retrocopy	retro_mmul_11,
Monodelphis domestica	ENSMODG00000019028	1 retrocopy	retro_mdom_1708,
Mustela putorius furo	ENSMPUG00000013296	1 retrocopy	retro_mputfur_1577,
Mus musculus	ENSMUSG00000063888	4 retrocopies	retro_mmus_2359, retro_mmus_3172, retro_mmus_3626, retro_mmus_777,
Otolemur garnettii	ENSOGAG00000012671	3 retrocopies	retro_ogar_1380, retro_ogar_3358, retro_ogar_3428,
Pteropus vampyrus	ENSPVAG00000008696	3 retrocopies	retro_pvam_1179, retro_pvam_1482, retro_pvam_975,
Rattus norvegicus	ENSRNOG00000016269	1 retrocopy	retro_rnor_2795,
Sorex araneus	ENSSARG00000005286	2 retrocopies	retro_sara_100, retro_sara_211,
Sarcophilus harrisii	ENSSHAG00000011219	1 retrocopy	retro_shar_216,
Sus scrofa	ENSSSCG00000026472	3 retrocopies	retro_sscr_198, retro_sscr_756, retro_sscr_807,
Ictidomys tridecemlineatus	ENSSTOG00000009841	2 retrocopies	retro_itri_1233, retro_itri_417,
Tarsius syrichta	ENSTSYG00000004848	16 retrocopies	retro_tsyr_1312, retro_tsyr_1340, retro_tsyr_1380, retro_tsyr_1399, retro_tsyr_1729, retro_tsyr_1914, retro_tsyr_1933, retro_tsyr_2161, retro_tsyr_357, retro_tsyr_455, retro_tsyr_469 , retro_tsyr_581, retro_tsyr_606, retro_tsyr_642, retro_tsyr_703, retro_tsyr_856,
Tarsius syrichta	ENSTSYG00000006100	25 retrocopies	retro_tsyr_1149, retro_tsyr_1200, retro_tsyr_1293, retro_tsyr_1297, retro_tsyr_1403, retro_tsyr_1598, retro_tsyr_1633, retro_tsyr_1850, retro_tsyr_1891, retro_tsyr_191, retro_tsyr_2109, retro_tsyr_2130, retro_tsyr_344, retro_tsyr_421, retro_tsyr_433, retro_tsyr_521, retro_tsyr_589, retro_tsyr_601, retro_tsyr_651, retro_tsyr_724, retro_tsyr_779, retro_tsyr_877, retro_tsyr_930, retro_tsyr_953, retro_tsyr_992,
Tursiops truncatus	ENSTTRG00000006971	6 retrocopies	retro_ttru_1194, retro_ttru_171, retro_ttru_361, retro_ttru_498, retro_ttru_528, retro_ttru_915,
Vicugna pacos	ENSVPAG00000008894	2 retrocopies	retro_vpac_386, retro_vpac_584,