RetrogeneDB ID: retro_ecab_960

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:74632838..74633996(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTCD
• Ensembl ID: ENSECAG00000009590
• Aliases: None
• Description: glutathione S-transferase, C-terminal domain containing [Source:HGNC Symbol;Acc:25806]

Sequence

>retro_ecab_960
GATACTTCACTACTTAAAAATGTATTGTCCCAGCATGTTCAAATCCAGATTATCTCGAGGCAAGAGCTTCCACAGATAGT
CCAGAATTGCTGTTTACCTGCAGTGGTAGAAGGACCAGACAGTTTCTACAGAGCAGGGCTCGCTGTTGTGCTGAGACACA
TCGTCCAGAAAGCATATGACGCAGAGCCCTCAAAGAAGGGGATCTTCGAGCTGCTGGATTTTAAGAAGACTTGTTTGAAG
GCCTGTGTTGAAGTTAGTCAGTAGACCAGGCTATGTAAACTTACCATCCCTTTAGCTATTGAGAATTTTGTCAAAGAGTC
TTGTGACCTGCACGCAGCTATCCCCACAGAAGTACTACAGCTAGAGAAAAAGCTCAGCGAGCCTGTTGGAGTGCGCAACG
ATGACAAACTCTGTGAGCAAAAGCTGAAGCAGCAGAAGGCTGCTGCAGTGGTGCCTGCTCTTGCCCAGGAGAAATTGAAG
GCCTGTAGACAGGAAACATCTGAGGACCAAGACCCTTCATCCCGCAGCCTGGAGCTGCAAGTGGCCTTCTCAACGCTCAC
GGTACAGGGGCACCCAGCTGCTCCCAACAGGGAGCCTGCTCACATCATACGAGCAGGCACCTGCGCGCTTCTGCTCCTGG
AGCACCTGTTTGCAGAAGGCCTGTACTTCGCCTTGGTAGACCTCGTACTTCTGCCCTGCAGCCATCACTTTTTGGTAATT
ATCCTCGAGAAGCTTTCTGAAAGGCTGGTAGAATTTCTGCTGCTGGCTGCCTGGTACCAGAGGGCTCAGGAGGTGCCAGG
AGTGAGAACAGCAGCTTCTTGCCATGGGACCTAGTTTCTCCACTTACCAGAGTTGCCGACCACCTCCAGCGAACAGCATC
CAAAATTCAGCAAGGCCCAGGAGCAGAGGAGCACAGCGACCCTTCGTTTATGTTTAGTGGGCCCAAGACCCACTATGACC
AAGTTAATGGAAAAGGGCATTGAAGTGATGTTTTCTCCCCACCCTTGCTCTGCTTGGACCCTTGACTGGAATAGACTTCC
TGCAGCAGTGAGCCCAAAAGATGGGAAGACGTCCAGTGATTGAGCGCTGAGGAAGCAGCAGGAGTTAAGCAACCTCGTCT
ACGTGGTGACACATCAGGCCAGGCCTGGGGACAGAATC

Alignment

ORF - retro_ecab_960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.85 %
• Parental protein coverage: 60.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DTSLLKNVLSQHVEIQIISRQELPLIVQNCCLPAVVESPDSFCRAGLAVVLRHIVQRAYDAEPSKKGILE
          DTSLLKNVLSQHV.IQIISRQELP.IVQNCCLPAVVE.PDSF.RAGLAVVLRHIVQ.AYDAEPSKKGI.E
Retrocopy DTSLLKNVLSQHVQIQIISRQELPQIVQNCCLPAVVEGPDSFYRAGLAVVLRHIVQKAYDAEPSKKGIFE

Parental  LLGFKKTCLKACAEVSQWTRLCELTIPLSIENFLKESCDQHPAIPTEILQLEKKLSEPVRVHNDDKLRRQ
          LL.FKKTCLKAC.EVSQ.TRLC.LTIPL.IENF.KESCD.H.AIPTE.LQLEKKLSEPV.V.NDDKL..Q
Retrocopy LLDFKKTCLKACVEVSQ*TRLCKLTIPLAIENFVKESCDLHAAIPTEVLQLEKKLSEPVGVRNDDKLCEQ

Parental  KLKQQKAAGAGPTLAQEKLKSQAHMQETSEDQDPSSQSLELQVAFSKLTVQEHPAAPNREPAHIRRAGAC
          KLKQQKAA...P.LAQEKLK..A..QETSEDQDPSS.SLELQVAFS.LTVQ.HPAAPNREPAHI.RAG.C
Retrocopy KLKQQKAAAVVPALAQEKLK--ACRQETSEDQDPSSRSLELQVAFSTLTVQGHPAAPNREPAHIIRAGTC

Parental  ALPPLEHVFAEGLYFTLADLVLLPCIHHFLVVICKKLSKRLVEFPLLAAWYQRVQEVPGVKTAASRCGIQ
          AL..LEH.FAEGLYF.L.DLVLLPC.HHFLV.I..KLS.RLVEF.LLAAWYQR.QEVPGV.TAAS..G..
Retrocopy ALLLLEHLFAEGLYFALVDLVLLPCSHHFLVIILEKLSERLVEFLLLAAWYQRAQEVPGVRTAASCHGT*

Parental  FLHLPELPTTSIEQHPKFSEA-AGAEEHSDPSFI-GGP-RPTMTKLMEKGIEVMFSPHPCPAWTLDWNRL
          FLHLPELPTTS.EQHPKFS.A..GAEEHSDPSF...GP.RPTMTKLMEKGIEVMFSPHPC.AWTLDWNRL
Retrocopy FLHLPELPTTSSEQHPKFSKA<PGAEEHSDPSFMFSGP>RPTMTKLMEKGIEVMFSPHPCSAWTLDWNRL

Parental  PAAVSPKEGKMSSDRALRKQQQLNNLVYVVTHQARPGDRI
          PAAVSPK.GK.SSD.ALRKQQ.L.NLVYVVTHQARPGDRI
Retrocopy PAAVSPKDGKTSSD*ALRKQQELSNLVYVVTHQARPGDRI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.00 RPM	6.38 RPM
SRP021940_cerebellum	0.00 RPM	11.74 RPM
SRP021940_embryo	0.13 RPM	24.17 RPM
SRP021940_placental_villous	0.29 RPM	6.30 RPM
SRP021940_synovial_membrane	0.00 RPM	9.20 RPM
SRP021940_testis	0.32 RPM	81.98 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_960 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_960 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009590	1 retrocopy	retro_ecab_960 ,