RetrogeneDB ID: retro_ecab_68

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:1704767..1706771(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000001472
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000010608
• Aliases: None
• Description: None

Sequence

>retro_ecab_68
TGTCCCAGTAACTTTATAAAACACATGAAATTGCACAGTGGAGTGGAATGCTACGAATGTACGGAGTGTGGGAAAGCTTT
CCGTTTTTCCTCATCCCTTCGAGTACATAAGAGGACACACAGTGAAGAGAAACCCTATGAATGTAAGGAGTGTGGGAAAG
CATTCACTAGTTCCTCATCTCTCAGAGCACACGTGAGGATGCACAGTGGGGAGAGACCCTTCCAGTGCCAGCAGTGTGGG
AAAGCCTTCACCTTTCAGTCCTCCCTTCGAGGACATATGAGAACACACACCGGGGAGAGACCCTATGAATGTCAGCACTG
CGGGAAAGCTTTCAGGGAGTCTCAGCATTTTCAAAGGCATGTGAGAATTCACAGTGGTGAGAAACCCTATGAATGTAAGG
AATGCGGGAAAGCCTTCAGTTATTCCTCATCCCTCCGAGAACATGTGAGGACACACACTGGGGAGAGGCCCTATGAGTGT
CAGCACTGTGGGAAAGCCTTCACTTGTCACTCCTCCTGCCGACGACATATGAGAACACACACCGAGGAGAGACCTTATGA
ATGTGAGCAATGTGGGAAAGCTTTCAAGATGCCTCAGAGTTTTCAAAGGCATATGAGAATTCACAGTGGTGAGAAACCCT
ATGAATGTAAGGTGTGTGGGAAAACCTTCAGGTGTTCCTCCTCACGTCGAAGACATGTGAGAACTCACAGTGAAGAGAAA
CCCCATGAGTGTAAGCAGTGTGGCAAAGCCTTCAAGTATTCTGCGTCCTTGGAAGTACACGTGAGAAGGCACAGTGGGGA
GAGACCCTACGCGTGTCAGCACTGTGGGAAAACTTTCATTCATCACTCCTACCTTCAAGTCCATGTGAGGGTACACAGTG
GGGACAGACCCTATGAATGTAAGCCATGTGGGAAAGCCTTCAGTTATCCGGCTAGCCTTCGAGTACATGTGAGAACACAC
ACAGAGGAGAGACCCTATGAGTGCCAGCACTGTGGGAAAGCCTTCAGGAGGCCTCAACATTTTCAGGCCCACATGAGAAT
GCACAGCGGTGTGAAACCCTATGAGTGTAGGGAATGTGGGAAAGCCTTCAGTTGTTCCTCATCACTTTGGATACATGTGA
GAAGTCACAGCAAAGAGAGACCCTATGAATGCAAGGAGTGTGGCAGAGCCTTCAGATATCCAGCAAACCTTCAAGTGCAT
GTCAGAATCCACAGTGGGGAGAGACCCTATGAATGTCAGCAATGTGGAAAAGCCTTCAAGAGACGTCAACATTTTCAAAG
TCATGTGAGAATGCACAGTGGTGTAAAACCCTATGAATGTATGGAATGTGGGAAAGCCTACAGTCGTCGCTCCTCCCTTC
AAGCACATGAGAGAAGCCACAGTGAGGAGAGACCCTATGAATGTCAGCAATGTGGGAAAGCCTTCAAGAAGCCTCAGCAC
TTTGAAAGACATGTGAGAATTCACAGTGGTATGAAACCTTATGAATGTAAGGAATGCGGGAAAGCCTTTAGTTGTTCCTC
AACACTTCGAATCCATGGGAGGACTCACACCGGAGAGAAACGCTATGAATGTAAGGAATGTGGCAAAGCCTTCAGACATT
CCTCATCCCTGCAGGTGCATGTGAGGATGCACAGTGGGGAGAGGCCCTATGCATGCAAGGAATGTGGGAAAGCCTTCACT
CGTCACACTGGCCTTCAACTACACGCCAGAACCCACAGTGGAGAGAGGCCCTATGAGTGTCAGCAATGTGGGAAAGCCTT
CAGTCGTCACTCCAACCTACAAGTACATGCCAGAAGCCACAGTGTGGAGAGACCTTATGAATGTCAACAATGTGGGAAAG
CTTTTAGTCGTCACACTGGCCTCCAACTACATGCCAGAACCCACAGTGGGGAGACACCCTATGAATGTCAGCAATGTAGG
AAAGCTTTCATGCAGCCTCAACAGTTTCAACGTCATCTCAGAACCCATGATGGGCAGAGGGGTATTAATGTCAGTAATGT
GGGA

Alignment

ORF - retro_ecab_68 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.88 %
• Parental protein coverage: 90.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSALQRHERTHIGEKPYKCKKCNKAFTSSSSLQVHERNHTGKKPYECKKCGKAFHFPSSLRSHETIHTGE
          PS....H...H.G...Y.C..C.KAF..SSSL.VH.R.H...KPYECK.CGKAF...SSLR.H...H.GE
Retrocopy PSNFIKHMKLHSGVECYECTECGKAFRFSSSLRVHKRTHSEEKPYECKECGKAFTSSSSLRAHVRMHSGE

Parental  KPYECKKCSKEFIFLSSLRRHERIHTGERPYECKKCSKAFCYPSSLQIHERIHTGEKPYECKKCSKAFTF
          .P..C..C.K.F.F.SSLR.H.R.HTGERPYEC..C.KAF......Q.H.RIH.GEKPYECK.C.KAF..
Retrocopy RPFQCQQCGKAFTFQSSLRGHMRTHTGERPYECQHCGKAFRESQHFQRHVRIHSGEKPYECKECGKAFSY

Parental  PSAFQRHESTHIREKPHECKNCSKTFSSSRALQIHDRTHSGEKIYECKKCSKAFTSPSALRLHERIHTGE
          .S....H..TH..E.P.EC..C.K.F........H.RTH..E..YEC..C.KAF..P.....H.RIH.GE
Retrocopy SSSLREHVRTHTGERPYECQHCGKAFTCHSSCRRHMRTHTEERPYECEQCGKAFKMPQSFQRHMRIHSGE

Parental  KPYECKKCSKAFTFSASLRKHERTHTREKPYEYNILGKKALRFPSSLQIYERTCTGEKPYKCQNCSKAFT
          KPYECK.C.K.F..S.S.R.H.RTH..EKP.E....GK.A.....SL....R...GE.PY.CQ.C.K.F.
Retrocopy KPYECKVCGKTFRCSSSRRRHVRTHSEEKPHECKQCGK-AFKYSASLEVHVRRHSGERPYACQHCGKTFI

Parental  SSSSLRVHERIHTGEKPYECKECGKAFRALASLQSHMIFHTGDGPYKCKECEKAFLSPSLLEIHERRHTG
          ..S.L.VH.R.H.G..PYECK.CGKAF...ASL..H...HT...PY.C..C.KAF..P.....H.R.H.G
Retrocopy HHSYLQVHVRVHSGDRPYECKPCGKAFSYPASLRVHVRTHTEERPYECQHCGKAFRRPQHFQAHMRMHSG

Parental  EKPYECKYCSKAFSLPSVLEIHERTHTGEKPYQCKECGKAFIALTNLRVHMVTHTGDGPYKCKECGKVFI
          .KPYEC..C.KAFS..S.L.IH.R.H..E.PY.CKECG.AF....NL.VH...H.G..PY.C..CGK.F.
Retrocopy VKPYECRECGKAFSCSSSLWIHVRSHSKERPYECKECGRAFRYPANLQVHVRIHSGERPYECQQCGKAFK

Parental  YPSLFQRHERSHTGEKPYECKECGKVFSLYAYLEKHKRTHTGGTPYVCKECGKAIISLKLFQIHERSHTR
          ....FQ.H.R.H.G.KPYEC.ECGK..S....L..H.R.H....PY.C..CGKA......F..H.R.H..
Retrocopy RRQHFQSHVRMHSGVKPYECMECGKAYSRRSSLQAHERSHSEERPYECQQCGKAFKKPQHFERHVRIHSG

Parental  EKSYECKKCNKAFTCPSSLRVHGRTHTGEKPYECKECGKAFRARSSLRSHVMLHTGDGPYKCKECGKAFI
          .K.YECK.C.KAF.C.S.LR.HGRTHTGEK.YECKECGKAFR..SSL..HV..H.G..PY.CKECGKAF.
Retrocopy MKPYECKECGKAFSCSSTLRIHGRTHTGEKRYECKECGKAFRHSSSLQVHVRMHSGERPYACKECGKAFT

Parental  SPSSLQRHERSHTEEKPYECKKCSKAFSYPYSLRVHERTHTGEKPYECKECGKAFIALTNLQSHMMRHTG
          ....LQ.H.R.H..E.PYEC..C.KAFS....L.VH.R.H..E.PYEC..CGKAF...T.LQ.H...H.G
Retrocopy RHTGLQLHARTHSGERPYECQQCGKAFSRHSNLQVHARSHSVERPYECQQCGKAFSRHTGLQLHARTHSG

Parental  DGPYKCKECEKAFISPSLLQIHGRSHTGEK
          ..PY.C..C.KAF..P...Q.H.R.H.G..
Retrocopy ETPYECQQCRKAFMQPQQFQRHLRTHDGQR

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	0.59 RPM	1.12 RPM
SRP021940_cerebellum	6.13 RPM	1.51 RPM
SRP021940_embryo	7.19 RPM	2.07 RPM
SRP021940_placental_villous	0.63 RPM	0.87 RPM
SRP021940_synovial_membrane	1.10 RPM	0.63 RPM
SRP021940_testis	5.12 RPM	1.92 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_68 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_68 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_68 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008838	1 retrocopy	retro_acar_51,
Anolis carolinensis	ENSACAG00000023302	2 retrocopies	retro_acar_3, retro_acar_34,
Anolis carolinensis	ENSACAG00000026389	2 retrocopies	retro_acar_13, retro_acar_4,
Anolis carolinensis	ENSACAG00000026721	1 retrocopy	retro_acar_23,
Anolis carolinensis	ENSACAG00000026996	1 retrocopy	retro_acar_22,
Anolis carolinensis	ENSACAG00000027062	1 retrocopy	retro_acar_29,
Ciona savignyi	ENSCSAVG00000007589	2 retrocopies	retro_csav_30, retro_csav_31,
Equus caballus	ENSECAG00000010608	1 retrocopy	retro_ecab_68 ,
Equus caballus	ENSECAG00000021667	1 retrocopy	retro_ecab_560,
Equus caballus	ENSECAG00000023688	1 retrocopy	retro_ecab_75,
Macaca mulatta	ENSMMUG00000013571	1 retrocopy	retro_mmul_248,