RetrogeneDB ID: retro_tsyr_1907

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_65189:10004..10728(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSTSYG00000010749
• Aliases: None
• Description: calponin 3, acidic [Source:HGNC Symbol;Acc:2157]

Sequence

>retro_tsyr_1907
ATTGCTTCCAAGTATGATCATCAGGCAGAAGAAGATCTTCACAATTGGATAGAAGAGGTGACAGGCATGAATATTGGCAC
CAATTTCTAGCTGGGCCTCAAGGATAGCATCATCCTCTGTGAACTCATAAACAAGCTGCAGCCAGGCTCAGTGAAGGTCA
AAGAGTCCTCATTAAACTGGCCTAGTTGGAGAATATTGACAACTTTATTAAAGCTATACAGGCTTATGGTATGAAGCCAC
ATGACATATTTGAGGCAAATGATCTTTTTGAGAATGGAAACACAACCCAAGTTCAGACTACTCTGGTGGCTCTTGCTGGT
CTGGCTAAAACAAAAGGATTCCATACAACGATTCACATCAGCGTTAAGTATTCAGAAAAACAAACAAGACGTTTTGGTGA
AGGAAAATTAAAAGCTGGCCAAAGTGTAACTGGTTTGCAGATGGGAACCAACAAATGTGCCAGCCAGGTAGGTATGATGA
CTTATGGGACTAGGAGGCACTTTTATGATCCCAAGATGCAAACTGACAGACCTTTTGACCAGACCACAGTTAGCCTGCAG
GTGGGCACTAACAAAGAAGCCAGCCAGGTGGGATGTTAGCACCAGGTACCAGAAGAGACATCTACGATCAGAAGCAAACA
TTACAACCTGTGAACAACTCGACAATCTCTCTTCAGATGAGTACCAACAAAGTTACTTCCCAGAAAGGAATGAGTGTATA
TGGG

Alignment

ORF - retro_tsyr_1907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.53 %
• Parental protein coverage: 80.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IASKYDHQAEEDLRNWIEEVTGMSIGTNFQLGLKDGIILCELINKLQPGSVKKVNESSLNWPQ-LENIGN
          IASKYDHQAEEDL.NWIEEVTGM.IGTNF.LGLKD.IILCELINKLQPGSVK.V.ESSLNWP..LENI.N
Retrocopy IASKYDHQAEEDLHNWIEEVTGMNIGTNF*LGLKDSIILCELINKLQPGSVK-VKESSLNWPS<LENIDN

Parental  FIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTIDIGVKYAEKQTRRFDEGKLK
          FIKAIQAYGMKPHDIFEANDLFENGN.TQVQTTLVALAGLAKTKGFHTTI.I.VKY.EKQTRRF.EGKLK
Retrocopy FIKAIQAYGMKPHDIFEANDLFENGNTTQVQTTLVALAGLAKTKGFHTTIHISVKYSEKQTRRFGEGKLK

Parental  AGQSVIGLQMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQMGTNKGASQ-AGMLAPGTRRD
          AGQSV.GLQMGTNKCASQ.GM..YGTRRH.YDPKMQTD.PFDQTT.SLQ.GTNK.ASQ..GMLAPGTRRD
Retrocopy AGQSVTGLQMGTNKCASQVGMMTYGTRRHFYDPKMQTDRPFDQTTVSLQVGTNKEASQ<GGMLAPGTRRD

Parental  IYDQKLTLQPVDNSTISLQMGTNKVASQKGIHHIG
          IYDQK.TLQPV.NSTISLQM.TNKV.SQKG....G
Retrocopy IYDQKQTLQPVNNSTISLQMSTNKVTSQKGMSVYG

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_1907 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 11 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Equus caballus	ENSECAG00000020188	1 retrocopy	retro_ecab_655,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Nomascus leucogenys	ENSNLEG00000011207	5 retrocopies	retro_nleu_122, retro_nleu_1342, retro_nleu_2698, retro_nleu_480, retro_nleu_668,
Pan troglodytes	ENSPTRG00000000979	15 retrocopies	retro_ptro_1061, retro_ptro_1149, retro_ptro_1247, retro_ptro_1447, retro_ptro_1505, retro_ptro_1554, retro_ptro_1871, retro_ptro_215, retro_ptro_2323, retro_ptro_2377, retro_ptro_2831, retro_ptro_2894, retro_ptro_3007, retro_ptro_483, retro_ptro_653,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Tarsius syrichta	ENSTSYG00000001645	2 retrocopies	retro_tsyr_1911, retro_tsyr_950,
Tarsius syrichta	ENSTSYG00000010749	2 retrocopies	retro_tsyr_1458, retro_tsyr_1907 ,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190, retro_vpac_449,