RetrogeneDB ID: retro_tsyr_488

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_1268:12831..13590(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH1
• Ensembl ID: ENSTSYG00000014777
• Aliases: None
• Description: mitochondrial carrier 1 [Source:HGNC Symbol;Acc:17586]

Sequence

>retro_tsyr_488
AAGTACATTGTGCAAGTGGATGGTAAGATAGGGCTGTTCCAAGGCCTGAGCCTCTGACTGATGTCCAGCACCCTCTCCAC
TGGGACCCAGGGCAGCATGAAGAAGGTGTTGCCTCCAGATGAGATTGAGCAGGTTTCCAGCAAGAATGATATGAAGACTT
CTCTGAAGAAAGTCGTGAAAGAGACCTCCTATGAGATGATGATACAGTATGTATCCTGTATGTTGGCCCACGCCCTGCAT
GTCATCTCAATGCGCTGCATGGTCCAGTTTATGTGCTGGGAGGGCAAGTACAGCAGTGTGCTGAGCTTCATTGGAAAGAT
ATTTAAAGAGGATGGGCTGCTGGGATTCTTTGTTGGCTTAATCCCTCACCTCCTGGGTGATGTGGTTATCTTGTGGGGCT
GTAACCTGCTGGCCCACTTCATCAATGCCTACCTGGTGGATGACAGCATGAGTGACACCCCAGGGGGACTGGGAAATGAC
CAGAATCCAGGTTCCCAGTTTATCCAGGCCCTGGCCATCTGGAGCTACACCAAGTTTGTGATGGGGATCACAGTGAGCAT
GCTGACCTACCCCTTCCTGCTGGTCGGTGACCTCATGACTGTGAACAACTGCAGGCAGCAGGCAGGGCTCCCCATTTACT
CCCCAGTGTTGAAATCCTGGATTCACTGCTGGAAGTACCTGAGTATACAGGGCCAGCTCTTCTGAGGCTCCAGCCTGCTT
TTCCTCCGGGTGTCATCAGGATCATGTTTTGTCCTGGAG

Alignment

ORF - retro_tsyr_488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KYIVQVDGKIGLFRGLSPRLMSNALSTVTRGSMKKVFPPDEIEQVSNKDDMKTSLKKVVKETSYEMMMQC
          KYIVQVDGKIGLF.GLS..LMS..LST.T.GSMKKV.PPDEIEQVS.K.DMKTSLKKVVKETSYEMM.Q.
Retrocopy KYIVQVDGKIGLFQGLSL*LMSSTLSTGTQGSMKKVLPPDEIEQVSSKNDMKTSLKKVVKETSYEMMIQY

Parental  VSRMLAHPLHVISMRCMVQFVGREAKYSGVLSSIGKIFKEEGLLGFFVGLIPHLLGDVVFLWGCNLLAHF
          VS.MLAH.LHVISMRCMVQF...E.KYS.VLS.IGKIFKE.GLLGFFVGLIPHLLGDVV.LWGCNLLAHF
Retrocopy VSCMLAHALHVISMRCMVQFMCWEGKYSSVLSFIGKIFKEDGLLGFFVGLIPHLLGDVVILWGCNLLAHF

Parental  INAYLVDDSVSDTPGGLGNDQNPGSQFSQALAIRSYTKFVMGIAVSMLTYPFLLVGDLMAVNNCGLQAGL
          INAYLVDDS.SDTPGGLGNDQNPGSQF.QALAI.SYTKFVMGI.VSMLTYPFLLVGDLM.VNNC..QAGL
Retrocopy INAYLVDDSMSDTPGGLGNDQNPGSQFIQALAIWSYTKFVMGITVSMLTYPFLLVGDLMTVNNCRQQAGL

Parental  PPYSPVFKSWIHCWKYLSVQGQLFRGSSLLFRRVSSGSCFALE
          P.YSPV.KSWIHCWKYLS.QGQLF.GSSLLF.RVSSGSCF.LE
Retrocopy PIYSPVLKSWIHCWKYLSIQGQLF*GSSLLFLRVSSGSCFVLE

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_488 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000137409	2 retrocopies	retro_hsap_3671, retro_hsap_856,
Gorilla gorilla	ENSGGOG00000003908	1 retrocopy	retro_ggor_2481,
Macaca mulatta	ENSMMUG00000021976	1 retrocopy	retro_mmul_1060,
Nomascus leucogenys	ENSNLEG00000010899	1 retrocopy	retro_nleu_423,
Pongo abelii	ENSPPYG00000016557	2 retrocopies	retro_pabe_3011, retro_pabe_691,
Pan troglodytes	ENSPTRG00000018115	1 retrocopy	retro_ptro_2490,
Tarsius syrichta	ENSTSYG00000014777	1 retrocopy	retro_tsyr_488 ,
Tursiops truncatus	ENSTTRG00000001966	2 retrocopies	retro_ttru_1101, retro_ttru_563,