RetrogeneDB ID: retro_tsyr_269

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_6744:31156..31856(+)
• Located in intron of: ENSTSYG00000008651

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPD
• Ensembl ID: ENSTSYG00000010395
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa) [Source:HGNC Symbol;Acc:5036]

Sequence

>retro_tsyr_269
CAGCAGGATAACGGTTAAATGTTTATTGGCAGCTTGAGCTGAGATACCAGCAAGAAGGATCTGAGTACTTGTCTCGATTT
CGGTAAGTTGTAGATGGCACCATTAAAACAGACTGCGTCCCTGGGCGATCAAGAGGATTTGGATTAGTGCTTTTCAAAGA
TGCCTCTAGTGCTGACAAGGTTTTAGAACTGAAGAACACATACCGGATGGCAAACTGACAGATCCCAAAAGGGCCAAAGC
TTTAGAAGAGAAAGAGCCCCCTAAAAAGGTTTTTTGTGGGCAGACGGAGCCCAGATACATCTGAAGAACAAATCAAAGAA
TATTTTGGAGCCTTTGGAGAGAATGAAAACATCGAACTTCCCATGGATACAAAAACAAACTAAAGAAGAGGATTTTGTTT
TATCACATACACAGATGAAGAACTGGTTAAAAAACTGTTAGAGAGCAGATACTATCAAATTGGTTCTGGGAAGTGTAAGA
TGAGTTGCACAACCCAAAGAGGTCTACAAGAGCAGCAGAAAGGAGGGAAAAGGGAGGCTGCCAGCGGCCAAGGTGGGGAG
AGGGGGCAGAGCCTTCGACACGGTCAAAACAAGGATTTAATAACTATTATGATCAATAATATGGAGATTACAACTGTGCC
TATGGTGGTGATCAAAACTATAGGGGCTATGGTGGATGAGATTATACTGGGTATAGCGAT

Alignment

ORF - retro_tsyr_269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.08 %
• Parental protein coverage: 84.12 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QREEWKMFIGGLSWDTTKK-DLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK-EH
          Q.....MFIG.LS.D.T.K.....Y.S.F..VVD.T.K.D...GRSRGFG.VLFK...S.DKV...K.EH
Retrocopy QQDNG*MFIGSLS*D-TSK<EGSEYLSRFR*VVDGTIKTDCVPGRSRGFGLVLFKDASSADKVLELK<EH

Parental  KLNGKVIDPKRAKAMKTKEPVKKIF-VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFIT
          ...GK..DPKRAKA...KEP.KK.F.VG..SPDT.EE.I.EYFG.FGE.E.IELPMD.KTN.RRGFCFIT
Retrocopy IPDGKLTDPKRAKALEEKEPPKKVF>VGRRSPDTSEEQIKEYFGAFGENENIELPMDTKTN*RRGFCFIT

Parental  FKEEEPVKKIMEKKYHNVGLSKCEIKVAMSKEQYQQQQQWGSRGGFAGRAR-GRGGGPSQNWNQGYSNYW
          ...EE.VKK..E..Y...G..KC...........Q.QQ..G.R....G....G.G..PS....QG..NY.
Retrocopy YTDEELVKKLLESRYYQIGSGKCKMS-CTTQRGLQEQQKGGKREAASGQGG<GEGAEPSTRSKQGFNNYY

Parental  NQGYGNYGY---NSQGYGGYGGYDYTGYNN
          .Q.YG.Y.......Q.Y.GYGG.DYTGY..
Retrocopy DQ*YGDYNCAYGGDQNYRGYGG*DYTGYSD

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_269 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015165	1 retrocopy	retro_cjac_2796,
Dipodomys ordii	ENSDORG00000012507	1 retrocopy	retro_dord_649,
Homo sapiens	ENSG00000138668	1 retrocopy	retro_hsap_4689,
Gorilla gorilla	ENSGGOG00000026760	1 retrocopy	retro_ggor_2916,
Loxodonta africana	ENSLAFG00000016483	1 retrocopy	retro_lafr_686,
Pan troglodytes	ENSPTRG00000016215	1 retrocopy	retro_ptro_3116,
Sarcophilus harrisii	ENSSHAG00000013312	1 retrocopy	retro_shar_752,
Tarsius syrichta	ENSTSYG00000010395	3 retrocopies	retro_tsyr_1092, retro_tsyr_2070, retro_tsyr_269 ,
Tarsius syrichta	ENSTSYG00000012949	2 retrocopies	retro_tsyr_1480, retro_tsyr_2122,
Tursiops truncatus	ENSTTRG00000007592	1 retrocopy	retro_ttru_1913,
Vicugna pacos	ENSVPAG00000004374	2 retrocopies	retro_vpac_484, retro_vpac_97,