RetrogeneDB ID: retro_tsyr_1004

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_273194:2891..3435(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPC
• Ensembl ID: ENSTSYG00000003305
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein C (C1/C2) [Source:HGNC Symbol;Acc:5035]

Sequence

>retro_tsyr_1004
ATCAGGAATCTTAACACTCTTGTGGTCAAGAAGTCTGATGTGGAGGCAATTTTTTCGAAGTGTGGCAAAATTGTGAGTTG
CTCTATTCATAAGAGCTTTGCTTTCATTCAATATGTTAATGAGAGACATGCCCAGGCTGCTGTAGCAGGAGAGGATGGCA
GAATGATTGCTGGCCAGGTTTTAGATACTAATCTGGCTCCAGAGCCGAAAGTGAACCAAGGAAAAGCAGGGTGTGAAACA
ATCTGCAGCGGAAACGTACGGGTCAGTACCAGAACACCCTTCTCTGTCCTCTCTACTCAGCTCCTCTTTTGACTTGGACT
ACAACTTTCAGCGGGATTATTATGACAGGATGTACGGTTACCCAGCACGAGTTCCTCCTCCTCCTATTGCTCGGGCTGTA
GTGCCCTCAAAACGCCAGTGTGTATCAGGAAACACCTCACGAAGGGGCAAAAGTGGCTTCAATTCTAAGAGTGGTCAGCG
AGGATCTTCTTCCAAGTCTGGAAAGTTGAAAGGTAATGACTTTCAGGCCATTAAGAAGGATTTG

Alignment

ORF - retro_tsyr_1004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.43 %
• Parental protein coverage: 59.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPK
          I.NLNTLVVKKSDVEAIFSK.GKIV.CS.HK.FAF.QYVNER.A.AAVAGEDGRMIAGQVLD.NLA.EPK
Retrocopy IRNLNTLVVKKSDVEAIFSKCGKIVSCSIHKSFAFIQYVNERHAQAAVAGEDGRMIAGQVLDTNLAPEPK

Parental  VNRGKA-GVKRSAAEMYGSVPEHPSPSPLLSSSFDLDYDFQRDYYDRMYSYPARVPPPPPIARAVVPSKR
          VN.GKA.GVK.SAAE.YGSVPEHPS.S.LLSSSFDLDY.FQRDYYDRMY.YPARV.PPPPIARAVVPSKR
Retrocopy VNQGKA>GVKQSAAETYGSVPEHPSLSSLLSSSFDLDYNFQRDYYDRMYGYPARV-PPPPIARAVVPSKR

Parental  QRVSGNTSRRGKSGFNSKSGQRGSSSKSGKLKGDDIQAIKKEL
          Q.VSGNTSRRGKSGFNSKSGQRGSSSKSGKLKG.D.QAIKK.L
Retrocopy QCVSGNTSRRGKSGFNSKSGQRGSSSKSGKLKGNDFQAIKKDL

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_1004 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 15 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005504	1 retrocopy	retro_cfam_1140,
Homo sapiens	ENSG00000092199	2 retrocopies	retro_hsap_1624, retro_hsap_3740,
Gorilla gorilla	ENSGGOG00000023015	1 retrocopy	retro_ggor_1046,
Macaca mulatta	ENSMMUG00000014809	4 retrocopies	retro_mmul_1112, retro_mmul_205, retro_mmul_468, retro_mmul_503,
Mustela putorius furo	ENSMPUG00000000164	2 retrocopies	retro_mputfur_231, retro_mputfur_241,
Mus musculus	ENSMUSG00000060373	1 retrocopy	retro_mmus_1388,
Nomascus leucogenys	ENSNLEG00000014362	2 retrocopies	retro_nleu_1828, retro_nleu_59,
Oryctolagus cuniculus	ENSOCUG00000015029	1 retrocopy	retro_ocun_138,
Otolemur garnettii	ENSOGAG00000012543	1 retrocopy	retro_ogar_165,
Pongo abelii	ENSPPYG00000005593	6 retrocopies	retro_pabe_1116, retro_pabe_1263, retro_pabe_1342, retro_pabe_2, retro_pabe_722, retro_pabe_780,
Pan troglodytes	ENSPTRG00000006118	2 retrocopies	retro_ptro_1089, retro_ptro_2539,
Rattus norvegicus	ENSRNOG00000011621	1 retrocopy	retro_rnor_922,
Tupaia belangeri	ENSTBEG00000011514	11 retrocopies	retro_tbel_1738, retro_tbel_2114, retro_tbel_2475, retro_tbel_2838, retro_tbel_2849, retro_tbel_3094, retro_tbel_3293, retro_tbel_3776, retro_tbel_3903, retro_tbel_3937, retro_tbel_818,
Tarsius syrichta	ENSTSYG00000003305	3 retrocopies	retro_tsyr_1004 , retro_tsyr_1326, retro_tsyr_1411,
Tursiops truncatus	ENSTTRG00000016055	2 retrocopies	retro_ttru_1299, retro_ttru_1490,