RetrogeneDB ID: retro_tsyr_331

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_8454:30442..31159(-)
• Located in intron of: ENSTSYG00000010779

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFC3
• Ensembl ID: ENSTSYG00000009501
• Aliases: None
• Description: replication factor C (activator 1) 3, 38kDa [Source:HGNC Symbol;Acc:9971]

Sequence

>retro_tsyr_331
TATGGACCATCAGGTGCTGAAAAAAAGACAAGAATTATGTGCATTCTATGTGAACTTTATGGTGTTGGAGGGGAAAAATT
GAGAATTGAACATCCGACCATCACAACTTCATCTAAAAAAAAAATTGAAATCAGCACCATTGCAACTAATTATCGCCTTG
AACTTAATCCCAGTGATGCTGGACATAGTGACTAGATAGTAATTTGGGAGATGTTGAAAACGGTGGCACAGTCACAGCAA
CTTGAAACAAACTCTCAAAGAAATTTTCAAGTGGTATTATTGACAGAAGTTGACGTACTCACCAAAGATGCTCAACACGC
CTTGCAAAGAACTGTGGAAAAGCACATGTCCACCTGCAGATTGGTCCTGTGCTGCAATTCTCCATTTAAAGTGATACCAC
CTATTCGTAGTAGGTGCTTGACAGTTTGTGTGCCTGCTCCCAGCATTAAAGATATTTGCCATGTGTTGTCTACTGTGGTT
AAGAAGGAAAGTCTGAATCTTCCCTCAGAACCGGCTCATAGAATAGCAGGGAAGTCTTGTTGAAATCTCAGGAAAGTCCT
ACTCATGTGTGTAGCCTGCAGAGTGTAGCAGTATCATTTTACTGTAGATCAAGAAACCCCTGAGACAGATAGGGAGGTCT
ATCTGAAGGAGACTGCGAATGCTGTTGTCAGCCAGCAAACTCCACAAAGGCTCCTTGAAGCTTCTAACTCTCTGTAT

Alignment

ORF - retro_tsyr_331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.33 %
• Parental protein coverage: 67.13 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YGPSGAGKKTRIMCILRELYGVGVEKLRIEHQTITTPSKKKIEISTIASNYHLEVNPSDAGNSDRVVIQE
          YGPSGA.KKTRIMCIL.ELYGVG.EKLRIEH.TITT.S....EISTIA.NY.LE.NPSDAG.SD..VI.E
Retrocopy YGPSGAEKKTRIMCILCELYGVGGEKLRIEHPTITTSSXXXXEISTIATNYRLELNPSDAGHSD*IVIWE

Parental  MLKTVAQSQQLETTSQRDFKVVLLTEVDKLTKDAQHALRRTMEKYMSTCRLILCCNSTSKVIPPIRSRCL
          MLKTVAQSQQLET.SQR.F.VVLLTEVD.LTKDAQHAL.RT.EK.MSTCRL.LCCNS..KVIPPIRSRCL
Retrocopy MLKTVAQSQQLETNSQRNFQVVLLTEVDVLTKDAQHALQRTVEKHMSTCRLVLCCNSPFKVIPPIRSRCL

Parental  AVRVPAPSIEDICHVLSTVCKKEGLNLPSELAHRIAEKSCRNLRKALLMCEACRVQQYPFTADQEIPETD
          .V.VPAPSI.DICHVLSTV.KKE.LNLPSE.AHRIA.KSC.NLRK.LLMC.ACRV.QY.FT.DQE.PETD
Retrocopy TVCVPAPSIKDICHVLSTVVKKESLNLPSEPAHRIAGKSC*NLRKVLLMCVACRV*QYHFTVDQETPETD

Parental  WEVYLRETANAIVSQQTPQRLLEVRGRLY
          .EVYL.ETANA.VSQQTPQRLLE....LY
Retrocopy REVYLKETANAVVSQQTPQRLLEASNSLY

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_331 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018380	1 retrocopy	retro_cjac_1611,
Cavia porcellus	ENSCPOG00000008739	1 retrocopy	retro_cpor_405,
Myotis lucifugus	ENSMLUG00000014088	1 retrocopy	retro_mluc_1754,
Mustela putorius furo	ENSMPUG00000001885	1 retrocopy	retro_mputfur_1073,
Nomascus leucogenys	ENSNLEG00000001169	1 retrocopy	retro_nleu_674,
Pongo abelii	ENSPPYG00000005272	1 retrocopy	retro_pabe_2420,
Tupaia belangeri	ENSTBEG00000004725	1 retrocopy	retro_tbel_4191,
Tarsius syrichta	ENSTSYG00000009501	2 retrocopies	retro_tsyr_1772, retro_tsyr_331 ,