RetrogeneDB ID: retro_ecab_61

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:22335488..22336925(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000001145
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000023794
• Aliases: None
• Description: None

Sequence

>retro_ecab_61
GCTTTTAGGAAAAGCTCATACCTCTCAAAACATGAGAGAATTCATTCTGCACAGAGACCTTACAAATGTAATGAGTGTGG
CAAAGCTTTTAATAAGTGCTTGAACCTTAGTAGACATCAGAAAATCCATACAAGAGAGAAACCATATAATTGTGATGTGG
GTGGCAAAATCTTTCATCAGAATTCAAACCTTGCAAGTCATCAGAGAATGGATACTGGCGAGAAACCTTACAAATGTAAT
GACTGCAGCAAGGCCTTTGCTAAACACTCAAGGCTTACTCAACATAAAAGAGTCCATACTGGAGAGAAACCTTACAAATG
TAATGAATGCAGCAAAGCCTTTGCTAGATGTTCAAGCCTTACTCAGCATAAGAGAATCCATACTGGAGAGAAACCTTACA
AATGTAGTGAATGCAGCAAAGCCTTTGCTGAACACTCAAAGCTTACTCAACATAAAAGAATCCATACTGGAGAAAAACCT
TACAAATGTAATGAATGCAAGAAAGCCTTTGCTAGACATTCAAGCCTTACTCAACATAAGAGAATCCATACTGGAGAGAA
ACCTTACAAATGTAATGAATGCAGCAAAGCCTTTCCTAGACACTCAATGCTTGCTCAACATAAAAGAATCCATACTGGAG
AAAAACCTTACAAATGTAATGAATGCAGCAAGTCCTTTGCTAAACGCTCAAGGCTTACTCAACATAAAAGAATCCATAAT
GGAGAGAAACCTTACAAATGTAGTGAATGCAGCAAAGCCTTTGCTAGACATTCAGGTCTTACTCAACATAAGATAATCCA
TACTGAAGAGAAACCTTGCAAATGTAGTAAGTGTGGCAAGGTATTTAGTCAAAAGTCAAGCCTTGAAAGTCATCAGAGAA
TTCATACTGGTGAGAAACCTTACAAATGTAATGAGTGTGGCAAATCTTTTACCCATTTTGTGTGCCTTAAAAGACATCAG
AAAATCCATACTGGAGAGAAACCTTACAAATGTAATGAGTGTGGCAAATCTTTTAACCGATTTGAAAGCCTTACAATACA
TCAGAAAATCCATACTGGAGAGAAACCTTACAAATGTAATGAGTGTGGTAAAGCCTTTATGGATGTTTCATACGTTACTC
GACATAAAAAAATCCATACTGGAGAGAAACCTTTCAAATGTAATGAGTGTGGCAAAACTTTTATGCAGGGTTCACATCTT
ACTCGACATAAGAAAATCCATACTGGAGAGAAACCTTACAAATGTAATGAGTGTGGCAAGGTCTGTAATCAAAAGTCAAA
CCTTGCAATTCATCAGAGAATTCATACTGGAGAGAAACCTTACAAATGTAATGAATGTGGCAAAGTGTTTGCTGAGCGTT
CAAGACTTACTCAGCATAAGAGAATCCATACTGGAGAGAAACCTTTCAAATGTACTGAGTGTGGCAAAACTTTTATG

Alignment

ORF - retro_ecab_61 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.12 %
• Parental protein coverage: 56.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SNLTIHQRTHTGEKPYKCNECGKAFMERSSLTQHTRIHSGEKPYSCKECGKAFNQSSNLVIHQIIHTGEK
          S.L..H.R.H....PYKCNECGKAF.....L..H..IH..EKPY.C...GK.F.Q.SNL..HQ...TGEK
Retrocopy SYLSKHERIHSAQRPYKCNECGKAFNKCLNLSRHQKIHTREKPYNCDVGGKIFHQNSNLASHQRMDTGEK

Parental  PYKCNVCGKAFNVCSSLTRHQTIHTGEKPYKCTQCGKAFSHCSTLANHQRIHSDERPYKCNECGRAFNRF
          PYKCN.C.KAF...S.LT.H...HTGEKPYKC..C.KAF..CS.L..H.RIH..E.PYKC.EC..AF...
Retrocopy PYKCNDCSKAFAKHSRLTQHKRVHTGEKPYKCNECSKAFARCSSLTQHKRIHTGEKPYKCSECSKAFAEH

Parental  SNLTRHQRIHTGEKPYKCNVCGKDFMIRSHLWSHERIHTGEKPYKCNECGKAFSERSNLAQHKRIHTGEK
          S.LT.H.RIHTGEKPYKCN.C.K.F...S.L..H.RIHTGEKPYKCNEC.KAF...S.LAQHKRIHTGEK
Retrocopy SKLTQHKRIHTGEKPYKCNECKKAFARHSSLTQHKRIHTGEKPYKCNECSKAFPRHSMLAQHKRIHTGEK

Parental  PYKCNECGKDFTTRSHLWGHERIHTGEKPYKCNECGKAFTGSSNLTQHKKIHTGEKPYKCTVCGKAFSQN
          PYKCNEC.K.F..RS.L..H.RIH.GEKPYKC.EC.KAF...S.LTQHK.IHT.EKP.KC..CGK.FSQ.
Retrocopy PYKCNECSKSFAKRSRLTQHKRIHNGEKPYKCSECSKAFARHSGLTQHKIIHTEEKPCKCSKCGKVFSQK

Parental  SSLIVHQRIHTGEKPYKCHECGKAFKQSETLQRRTKIHTEERPYKCKECGKAFNRYSNFTIHQRIHTGEK
          SSL..HQRIHTGEKPYKC.ECGK.F.....L.R..KIHT.E.PYKC.ECGK.FNR....TIHQ.IHTGEK
Retrocopy SSLESHQRIHTGEKPYKCNECGKSFTHFVCLKRHQKIHTGEKPYKCNECGKSFNRFESLTIHQKIHTGEK

Parental  PYKCKECGQAFTWCSSLTIHQRIHTGEKPYKCKVCCKAFNQYSNLTKHQRIHTGEKPYKCKECCKAFTWY
          PYKC.ECG.AF...S..T.H..IHTGEKP.KC..C.K.F.Q.S.LT.H..IHTGEKPYKC.EC.K.....
Retrocopy PYKCNECGKAFMDVSYVTRHKKIHTGEKPFKCNECGKTFMQGSHLTRHKKIHTGEKPYKCNECGKVCNQK

Parental  TSLTIHQRIHTGEKPYKCKEC-SIFNQYSYLTIHQRIHTGEKPYKCKECGKAF
          ..L.IHQRIHTGEKPYKC.EC...F...S.LT.H.RIHTGEKP.KC.ECGK.F
Retrocopy SNLAIHQRIHTGEKPYKCNECGKVFAERSRLTQHKRIHTGEKPFKCTECGKTF

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	0.53 RPM	2.30 RPM
SRP021940_cerebellum	0.16 RPM	1.87 RPM
SRP021940_embryo	1.51 RPM	4.58 RPM
SRP021940_placental_villous	0.05 RPM	1.68 RPM
SRP021940_synovial_membrane	0.00 RPM	2.33 RPM
SRP021940_testis	0.06 RPM	1.92 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_61 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_61 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_61 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023794	1 retrocopy	retro_ecab_61 ,
Macaca mulatta	ENSMMUG00000003688	1 retrocopy	retro_mmul_44,
Otolemur garnettii	ENSOGAG00000005643	1 retrocopy	retro_ogar_19,
Otolemur garnettii	ENSOGAG00000029638	2 retrocopies	retro_ogar_105, retro_ogar_193,
Pelodiscus sinensis	ENSPSIG00000004688	1 retrocopy	retro_psin_20,
Pelodiscus sinensis	ENSPSIG00000008115	1 retrocopy	retro_psin_11,