RetrogeneDB ID: retro_tsyr_603

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_148139:966..1661(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTSYG00000002858
• Aliases: None
• Description: None

Sequence

>retro_tsyr_603
AGGAAGGGGAAAGCGTTCCTGGAGCCTTTGTTTCTTGAGGCACCCAGATCTGTGGATTGGAGAGAGAAAGGCTACGTGAC
TCCTGTGAAGAATCAGGGTGAATGTGGTTCATGTTGGGCTTTTAGTGCAACTGGTACCAGTTTTCAGATGTTCCGGAAAA
CTGGTAAACTTATCTCACTGAGTGAGCAGAACCTGGTGGACTGTTCTCAGGCTCAAGGCAATGAGGGCTGCAATGGTGGC
CTGAAGGGTAATGCCTTCCAGTATATAAAGAGAACAGAGGCCTGGACTCTGAGGCATCCTATCCATACACAGGAAAGGAT
GAAACCTGTAAGTACAAGCCTGAGTATTCTGGCGCTAATGACACTGGCTTCGTGGACATCCCAGTTGGAGAGAAGGCCCT
GATGAGGGCAGTGGCATTTTGGGGGCCCATCTCTGTTGCCGTTGATGCAGGCCATGAGTCCTTCCAGTTCTATAAAGAAG
GTATTTATTTTGTGCCAGACTGCAGCAGTGAAGACTTGGATCATGGTGTTCTGGTAGTTGGCTACAACTATGAAGGAACA
GACTCAGATAACAGTAAATACTGGATTGTGAAGAACAGCTAGGGTACAGGCTGGGTCATGGATGGCTACATAAAGATGGC
CAGAGAGCCGGAGAACAACTCTGGAATCGCCCCAGCAGCCAGCTATCCCGTCGTG

Alignment

ORF - retro_tsyr_603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.1 %
• Parental protein coverage: 69.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKGKAFQAPPLSDFPPSMDWRKKGFVTPVKFQGPCGSCWAFSATGALEGQMVWKTGQLVALSEQNLVDCS
          RKGKAF..P.....P.S.DWR.KG.VTPVK.QG.CGSCWAFSATG....QM..KTG.L..LSEQNLVDCS
Retrocopy RKGKAFLEPLFLEAPRSVDWREKGYVTPVKNQGECGSCWAFSATGT-SFQMFRKTGKLISLSEQNLVDCS

Parental  GPQGNLGCDGGWMESAFQYVL-ENGGLDAEEFYPYMAADEDCKYKPEYSAANDTGFIDIPEGENSLLSAV
          ..QGN.GC.GG....AFQY...EN.GLD.E..YPY...DE.CKYKPEYS.ANDTGF.DIP.GE..L..AV
Retrocopy QAQGNEGCNGGLKGNAFQYIK<ENRGLDSEASYPYTGKDETCKYKPEYSGANDTGFVDIPVGEKALMRAV

Parental  ATVGPISVAIDASQDSFQFYGEGIYYEPNCSKEKTNHAVLVVGYGHEGVKPDENKYWLVKNSWSTYWGLN
          A..GPISVA.DA...SFQFY.EGIY..P.CS.E...H.VLVVGY..EG...D..KYW.VKNS..T.W...
Retrocopy AFWGPISVAVDAGHESFQFYKEGIYFVPDCSSEDLDHGVLVVGYNYEGTDSDNSKYWIVKNS*GTGWVMD

Parental  GYIKMARDRNNNCGIASYASYPTV
          GYIKMAR...NN.GIA..ASYP.V
Retrocopy GYIKMAREPENNSGIAPAASYPVV

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_603 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000019810	1 retrocopy	retro_dord_197,
Macropus eugenii	ENSMEUG00000002168	2 retrocopies	retro_meug_1349, retro_meug_1567,
Macropus eugenii	ENSMEUG00000014293	1 retrocopy	retro_meug_1873,
Macropus eugenii	ENSMEUG00000016209	2 retrocopies	retro_meug_159, retro_meug_1727,
Myotis lucifugus	ENSMLUG00000003975	1 retrocopy	retro_mluc_2231,
Myotis lucifugus	ENSMLUG00000025440	1 retrocopy	retro_mluc_2399,
Macaca mulatta	ENSMMUG00000013861	1 retrocopy	retro_mmul_1669,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Petromyzon marinus	ENSPMAG00000003453	1 retrocopy	retro_pmar_7,
Tarsius syrichta	ENSTSYG00000002858	2 retrocopies	retro_tsyr_150, retro_tsyr_603 ,