RetrogeneDB ID: retro_ecab_937

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:74532490..74533438(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANKRD40
• Ensembl ID: ENSECAG00000012574
• Aliases: None
• Description: ankyrin repeat domain 40 [Source:HGNC Symbol;Acc:28233]

Sequence

>retro_ecab_937
ACCTGTGTACACCGGATATGTAAACACAGTCATGACCAGGTGGTCTCTAACTTGTTAAAATGAGCATCTGACAGAGAAAT
TCTTACCACAAAAGGAGAAATGCCAGTCCAATTAACATCAAGGAGAGAAATTAGGAAGATTATGGGAGTAGAAAATGATT
ATGATGAAGAAAACTACCCCCAGTTTAAGAAGGAGACAGACCTACCTTTTGTTCCTAATTGTTTGGCCAAGACAGACTTC
CATTTTATCTACAATCCCACAGTAGAGGATTCAGCCCAACTGCAGAATGGGGGCTCATCTTCACCTCCTGCATCACTTCT
TGTGGATGGCTCACCTCCGTTGCTCCTTCATAGGGACCCTCCCCTGCTGGGAACCTTTTTGTGGGACCACACCTCTTGAC
ACTGGTTCAGAACTAGGAGGTGTCTGCCCCCTCTGCCATACTCAGAACACCAGAAAGCACAAAACCGGAGACTGTTCGTT
AGTCACCAGGGAGTCACAGTCGCTCACTGTTCTCTTCTGTCCTGTCCAACCTGCCAGTGTTGCTGGAGCTGCAAAATGGG
ATGTTTACACGACTGCTGCCAGCATTCCCTCCATTTTTACTCACTGGAGCATTTCCATTTAATATGCAAGAGCTAGTACT
TAAGATGAGGGTTCAGAACCCATCTCTTTGAGAAAATGATTTTGTTAAAATTGAACTGGCCCTTCAGGAGCTTACCTACC
ACAAATTGCTCAGAATGACTTACTGTGCCCTGAGTGTTAATCCGGATAAGTGGAGATCAGAAAGGTATCCAGTGCTCTGG
TAAGAAAAGACAAAGATGTTGCTCAACTTCAAGATTTCCAAGAGTTGGAACTGATTCTAATGATAAGTGAAAATAATTTT
TCTTCAGAAATGCTGCATCCACACTGACTGAAAGGTCTTGCTACAACAAGAGAGCTTCAAAACTGACT

Alignment

ORF - retro_ecab_937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.81 %
• Parental protein coverage: 99.69 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TCLHWACKRNHGQVVSYLLKSGADKEILTTKGEMPVQLTSRREIRKIMGVEDDNDDDDNLPQLKKESELP
          TC.H..CK..H.QVVS.LLK...D.EILTTKGEMPVQLTSRREIRKIMGVE.D.D...N.PQ.KKE..LP
Retrocopy TCVHRICKHSHDQVVSNLLK*ASDREILTTKGEMPVQLTSRREIRKIMGVENDYDEE-NYPQFKKETDLP

Parental  FVPNYLANPAFPFIYTPAAEDSAQLQNGGPSTPPASPPADGSPPLLSPGNPPLLGAFPRDHTS-LALVQN
          FVPN.LA...F.FIY.P..EDSAQLQNGG.S.PPAS...DGSPPLL....PPLLG.F..DHTS.L.LVQN
Retrocopy FVPNCLAKTDFHFIYNPTVEDSAQLQNGGSSSPPASLLVDGSPPLLLHRDPPLLGTFLWDHTS<LTLVQN

Parental  GDVSAPSAILRAPESTKPGPVCQPPVSQSRSLFSSVPSKPPVSLEPQNGTYAGPAPAFQPFFFTGAFPFN
          ..VSAPSAILR.PESTKP..V...P.S.SRSLFSSV.S..PV.LE.QNG......PAF.PF..TGAFPFN
Retrocopy *EVSAPSAILRTPESTKPETVR*SPGSHSRSLFSSVLSNLPVLLELQNGMFTRLLPAFPPFLLTGAFPFN

Parental  MQELVLKVRIQNPSLRENDFIEIELDRQELTYQELLRVSCCELGVNPDQ-VEKIRKLPNTLVRKDKDVAR
          MQELVLK.R.QNPSL.ENDF..IEL..QELTY..LLR...C.L.VNPD..VE.IRK....LVRKDKDVA.
Retrocopy MQELVLKMRVQNPSL*ENDFVKIELALQELTYHKLLRMTYCALSVNPDK<VE-IRKVSSALVRKDKDVAQ

Parental  LQDFQELELVLTISENN-FLFRNAASTLTERPCYNRRASKLT
          LQDFQELEL.L.ISENN.F.FRNAASTLTER.CYN.RASKLT
Retrocopy LQDFQELELILMISENN<FFFRNAASTLTERSCYNKRASKLT

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	12.46 RPM
SRP021940_cerebellum	0.00 RPM	44.71 RPM
SRP021940_embryo	0.00 RPM	22.66 RPM
SRP021940_placental_villous	0.10 RPM	14.34 RPM
SRP021940_synovial_membrane	0.00 RPM	16.42 RPM
SRP021940_testis	0.00 RPM	22.51 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_937 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_937 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_937 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000012574	1 retrocopy	retro_ecab_937 ,
Rattus norvegicus	ENSRNOG00000002935	2 retrocopies	retro_rnor_1835, retro_rnor_755,
Tursiops truncatus	ENSTTRG00000000221	1 retrocopy	retro_ttru_824,