RetrogeneDB ID: retro_tsyr_2149

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_96179:5965..6959(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPK
• Ensembl ID: ENSTSYG00000001196
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein K [Source:HGNC Symbol;Acc:5044]

Sequence

>retro_tsyr_2149
GATGCTGTGGATGCTCAAATACCACACTATAAAGGAAGTGACTTTGACTGCGAGTTGAGACTGCTGATCATCAGAGTCTG
GCAGGAGGAATTATGGGGTCAAAGGTGCTAAAATTCAAGAACTTCGAGAGAACACTCAGACAACAATCAAGCTTTTCCAG
GAGTGCTGTCCTCATTCCACTGACAGAGTTGTTCTTATTGGAGGAAAGCATGATAGGGTTGTAGAGTGCATAAAGATCAT
CCTTGATCTTATATCTGAGTCTCCCATCAAAGGATGTGCACAACCTTATGATCCCAATTTTTATGATGAAACCTATGACT
ATGGTGGTTTTACAATGATATTCGATGACCGCCGTGGACGTCCAGTGGGATTTCCGATGCGGGGAAGAGGTGGTTTTGAC
AGAATGCCTCCTGGTGGGGGTGGGTGTCTTATGCCTCCTTCTAGAAGAGATTATGATGATATGAGCCCTCGTTGAGGACC
ACCGCCACCTCCTCCTGGACGAGGTGGCCGGGATGGTAGCAGAGCTCGGAATCTTCCTCTTCCTCCACCACCACCACCTA
GAGGAGGAGATCTAATGGCCTATGACAGAAGAGGAAGACCGGGAGACTGTTACGATGGCATGGTTGGTTTCAGTGCTAAC
GAAACTTGGGACTCTGCAATAGATATATGGAGCCCGTCAGAATGGCAGATGGCTTATGAACCACAGGGTGCCTCTGGATA
TGATTATTCCTATGCAGGGGGTCGTGGCTCTTATGGTGATCTTGGTGGACCTATTATTACTACTAAAGTAACTATTCCCA
AAGATTTGGCTGGATCTATTATTGGCAAAGGTGGTCAGCGGATTAAACAAATCCGTCATGAGTCGGGAGCTTCGATCAAA
ATTGATGAGCCTTTCGAAGGATCCGAAGATCAGATCATTACAATTACCGGAACACAGGACCAGATACAGAATGCACAGTA
TTTGCTGCAGAACAGTGTGAATTTTTTCTAAGAC

Alignment

ORF - retro_tsyr_2149 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.06 %
• Parental protein coverage: 71.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DAVECLNYQHYKGNDFDCELRLLI-HQSLAGGIIG-VKGAKIKELRENTQTTIKLFQECCPHSTDRVVLI
          DAV......HYKG.DFDCELRLLI.HQSLAGGI.G.VKGAKI.ELRENTQTTIKLFQECCPHSTDRVVLI
Retrocopy DAVDA-QIPHYKGSDFDCELRLLI<HQSLAGGIMG<VKGAKIQELRENTQTTIKLFQECCPHSTDRVVLI

Parental  GGKPDRVVECIKIILDLISESPIKGRAQPYDPNFYDETYDYGGFTMIFDDRRGRPVGFPMRGRGGFDRMP
          GGK.DRVVECIKIILDLISESPIKG.AQPYDPNFYDETYDYGGFTMIFDDRRGRPVGFPMRGRGGFDRMP
Retrocopy GGKHDRVVECIKIILDLISESPIKGCAQPYDPNFYDETYDYGGFTMIFDDRRGRPVGFPMRGRGGFDRMP

Parental  PGRGGRPMPPSRRDYDDMSPRRGPPPPPPGRGGRGGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDRYDG
          PG.GG..MPPSRRDYDDMSPR.GPPPPPPGRGGR.GSRARNLPLPPPPPPRGGDLMAYDRRGRPGD.YDG
Retrocopy PGGGGCLMPPSRRDYDDMSPR*GPPPPPPGRGGRDGSRARNLPLPPPPPPRGGDLMAYDRRGRPGDCYDG

Parental  MXXXXXXXXXXXXIDTWSPSEWQMAYEPQGGSGYDYSYAGGRGSYGDLGGPIITTQVTIPKDLAGSIIGK
          M............ID.WSPSEWQMAYEPQG.SGYDYSYAGGRGSYGDLGGPIITT.VTIPKDLAGSIIGK
Retrocopy MVGFSANETWDSAIDIWSPSEWQMAYEPQGASGYDYSYAGGRGSYGDLGGPIITTKVTIPKDLAGSIIGK

Parental  GGQRIKQIRHESGASIKIDEPLEGSEDRIITITGTQDQIQNAQYLLQNSVKQYAD
          GGQRIKQIRHESGASIKIDEP.EGSED.IITITGTQDQIQNAQYLLQNSV....D
Retrocopy GGQRIKQIRHESGASIKIDEPFEGSEDQIITITGTQDQIQNAQYLLQNSVNFF*D

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_2149 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 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000026	4 retrocopies	retro_dnov_1433, retro_dnov_1820, retro_dnov_2316, retro_dnov_2638,
Dipodomys ordii	ENSDORG00000016024	1 retrocopy	retro_dord_673,
Gorilla gorilla	ENSGGOG00000015500	2 retrocopies	retro_ggor_1764, retro_ggor_1866,
Loxodonta africana	ENSLAFG00000026567	1 retrocopy	retro_lafr_809,
Macaca mulatta	ENSMMUG00000018871	1 retrocopy	retro_mmul_2111,
Monodelphis domestica	ENSMODG00000008402	1 retrocopy	retro_mdom_1666,
Mus musculus	ENSMUSG00000021546	2 retrocopies	retro_mmus_1131, retro_mmus_2137,
Nomascus leucogenys	ENSNLEG00000003486	3 retrocopies	retro_nleu_1178, retro_nleu_1815, retro_nleu_973,
Otolemur garnettii	ENSOGAG00000007478	3 retrocopies	retro_ogar_2635, retro_ogar_2966, retro_ogar_3086,
Pongo abelii	ENSPPYG00000019327	3 retrocopies	retro_pabe_2105, retro_pabe_2106, retro_pabe_42,
Sarcophilus harrisii	ENSSHAG00000017109	1 retrocopy	retro_shar_820,
Tarsius syrichta	ENSTSYG00000001196	3 retrocopies	retro_tsyr_1664, retro_tsyr_1796, retro_tsyr_2149 ,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,