RetrogeneDB ID: retro_tsyr_2070

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_8639:35495..36308(+)
• Located in intron of: None

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_2070
CAGCAGGATGACGGTAAAATGCTTATTAGAGATTTCAACTGGGATACAAGCAAGAAGGACCTGACTGAGTACTTGTCTTG
ATTTGGGGAAGTTGTAGATTGCACCATTAAAACAGACCCTGTCACTGGGCCATCAAGAGGATTTGGATTCGTGCTTTTCA
AAGATGCTTCTAGTGTTGACAAGGTTTTGGAACTGAAAGAACACAAACTAGATGGCAAATTGATAGACCCCCCAAAGGGC
CAAAGCTTTAAGAACCCACCAAGTTTTTGTGAGTAGATTTAGCCCAGATACTTCTGAAGACCAAATTAAAGAATATTTTG
GAGCCTTTGGAGAGATTGAAAATATTGAGCTTCTCATGGATATAAAAACAAATTTTAAAAAAGAGAATTTTGTTTTATCA
CATATACAGATGAACAGCCAGTAAATAAATTATTAGAAAGCCGATATCATCAAATTGGTTCTAGGAAGTATGATATCAAA
GTTGCACAGTCCAAAGAGGTCTACAGGCAGCAGCAGCAGAAAGGAGGGAGAGGTGCTGCTGCTGGTGGCCCAGGCAGGGC
AAGGGGGCGTGGCCTAGGTCAGGGCCAAAACTGGAACCAAGGATTTAATAACTATTCTGATCAAGGATATAGAAATTACA
ATAGTGCCTATGGTGGTGATCAAAATTATAGTGGCTATGGCGTATATGATTATACTGGGTATAACTATGGAAACTATGGA
TGTGGTCAGGGACATGCAGACTGCAGTGGTCAACCAAGCACTTGGCACTACGTCTTGAGGGATGGCAATCAACAAAACTA
TCACCAGCCATAT

Alignment

ORF - retro_tsyr_2070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.04 %
• Parental protein coverage: 94.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QREEWKMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKL
          Q....KM.I....WDT.KKDL..Y.S.FGEVVDCT.K.DP.TG.SRGFGFVLFK...SVDKV...KEHKL
Retrocopy QQDDGKMLIRDFNWDTSKKDLTEYLS*FGEVVDCTIKTDPVTGPSRGFGFVLFKDASSVDKVLELKEHKL

Parental  NGKVID-PKRAKAMKTKEPVKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTN-KRRGF-CFIT
          .GK.ID.P.RAKA..T.......FV...SPDT.E..I.EYFG.FGE.E.IEL.MD.KTN.K...F.CFIT
Retrocopy DGKLID>PQRAKALRTHQ----VFVSRFSPDTSEDQIKEYFGAFGEIENIELLMDIKTNFKKENF<CFIT

Parental  FKEEEPVKKIMEKKYHNVGLSKCEIKVAMSKEQYQQQQQWGSRGGFAG---RARGRGGGPSQNWNQGYSN
          ...E.PV.K..E..YH..G..K..IKVA.SKE.Y.QQQQ.G.RG..AG...RARGRG.G..QNWNQG..N
Retrocopy YTDEQPVNKLLESRYHQIGSRKYDIKVAQSKEVYRQQQQKGGRGAAAGGPGRARGRGLGQGQNWNQGFNN

Parental  YWNQGYGNYGY---NSQGYGGYGGYDYTGYN--NY---YGYGDYSNQQSGYGKVSRRGGHQNSYKPY
          Y..QGY.NY.......Q.Y.GYG.YDYTGYN..NY....G..D.S.Q.S....V.R.G..QN...PY
Retrocopy YSDQGYRNYNSAYGGDQNYSGYGVYDYTGYNYGNYGCGQGHADCSGQPSTWHYVLRDGNQQNYHQPY

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_2070 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.

---

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,