RetrogeneDB ID: retro_ecab_581

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:35786547..35787395(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EHD3
• Ensembl ID: ENSECAG00000015195
• Aliases: None
• Description: EH-domain containing 3 [Source:HGNC Symbol;Acc:3244]

Sequence

>retro_ecab_581
GTCTACAGGGTGTATATTTGCCCCTTCTGGTTCCATCTGCTCCTCATCCCCAACAACTGCAAGATCTTCCAGGGCAAGAA
GCAGGACCTCTTCAAAGACATCCAGTCTCTTTCCCCAAACCCTGGCCTCAGGAAGCTCACTGACCTGAACAAGTGGGCAC
GGCTGGCAAGGTCCACGCCTACATCATCAGCTCCTTCAAGAAGATGCCTAATGTCTTCGGTAAAGAGAGCAAAAGGAAAG
AATTGGTGGACAACCTGGGGAGACCCACTAGAAGACTGAGTGGGAGCATCGGATGTCCCCTGGCAACTTTCCAAGACTCC
CGCAAGATGCAGGAACTTCCACATATCCAGGACTCCGTAAAGTGCCAGGCCTTGAAGCTCAAGCTGATGGATGTGATTAA
TGACATGCTAGCCAATGACATTGCCCGGTTGATGGTGATGGTGTGCCAGGAAGAGTCCCTGATGCCCTGCCAGGCTGCAA
AGGGCCGTGCCTTGGACGGCACCGTTAACAGGCTCTTTGGGCACAACTACTGCGAGGGGGGCGGCAAGGACATTTGATGA
CACTGAGTGAGTGGTGGACAAGGACAAGCCCACCTAAAAAGAGCTCTTTTACATGGCTAGTCACCTGTCAACTGCAAGGT
CGTGAGTGCCCGTGCCAAGAAAGAGATGGTGAAGTCCAAGCTGCACGATACCGTGCTGGGGGAGGTCTGGAAGCTGGCTG
ATGTGCACCAGGACAGGCTGCTGGACGATGAGGATTGTGCCCTGGACAGCCACTTCATCAAAGACAAGCTGGAGGGCGGC
AGGCTGCCCAGTGACCTGCCCCAAGACCTGATCACATCTAAGCAGAGG

Alignment

ORF - retro_ecab_581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.71 %
• Parental protein coverage: 52.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  VIRVYI-GFWSHPLLIPDNRKLFEAEEQDLFRDIQSLPRNAALRKLNDLIKRARLA-KVHAYIISSLKKE
          V.RVYI..FW.H.LLIP.N.K.F....QDLF.DIQSL..N..LRKL.DL.K.ARLA.KVHAYIISS.KK.
Retrocopy VYRVYICPFWFHLLLIPNNCKIFQGKKQDLFKDIQSLSPNPGLRKLTDLNKWARLA<KVHAYIISSFKK-

Parental  MPSVFGKENKKKELVNNLA-EIYGRIEREHQISPGDFPNV-KKMQDQLQAQDFSKFQPLKSKLLEAVDDM
          MP.VFGKE.K.KELV.NL..E.....E.EH..SPG.FP....KMQ.....QD..K.Q.LK.KL.....DM
Retrocopy MPNVFGKESKRKELVDNLG<ETH*KTEWEHRMSPGNFPRL>RKMQELPHIQDSVKCQALKLKLMDVINDM

Parental  LAHDIAQLMVLVRQEETQRPVQMVKGGAFEGTLHGPFGHGYGEGAGEGI-DDAEWVV-ARDKPMYDEIFY
          LA.DIA.LMV.V.QEE...P.Q..KG.A..GT....FGH.Y.EG.G..I.DD.E.VV..R..P.....F.
Retrocopy LANDIARLMVMVCQEESLMPCQAAKGRALDGTVNRLFGHNYCEGGGKDI>DDTE*VV>TRTSPPKKSSFT

Parental  TL-SPVDGKITGANAKKEMVRSKLPNSVLGKIWKLADIDKDGMLDDEEFALANHLIKVKLEGHELPNELP
          .L.SPV..K...A.AKKEMV.SKL...VLG..WKLAD...D..LDDE..AL..H.IK.KLEG..LP..LP
Retrocopy WL>SPVNCKVVSARAKKEMVKSKLHDTVLGEVWKLADVHQDRLLDDEDCALDSHFIKDKLEGGRLPSDLP

Parental  AHLLPPSKR
          ..L.....R
Retrocopy QDLITSKQR

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	53.84 RPM
SRP021940_cerebellum	0.00 RPM	130.92 RPM
SRP021940_embryo	0.03 RPM	23.55 RPM
SRP021940_placental_villous	0.00 RPM	18.28 RPM
SRP021940_synovial_membrane	0.00 RPM	12.16 RPM
SRP021940_testis	0.00 RPM	16.63 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_581 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_581 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_581 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015195	1 retrocopy	retro_ecab_581 ,
Monodelphis domestica	ENSMODG00000015505	1 retrocopy	retro_mdom_915,
Sarcophilus harrisii	ENSSHAG00000013011	1 retrocopy	retro_shar_114,
Tupaia belangeri	ENSTBEG00000010371	1 retrocopy	retro_tbel_4556,