RetrogeneDB ID: retro_ecab_153

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:160868234..160869162(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000014288
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000019445
• Aliases: None
• Description: None

Sequence

>retro_ecab_153
TTGATATAATTTGCACCTGGAGCTCATGGACACTATAGTCCTTTTGATGATAGGAATGGAATCATAGCCCATGCTTTTGG
ACTTGGACCTGGTATTGGAGGAGACGCACATTTTGATGAGGCTAAAATCTGGACTGAAAGCTGTAAAGACACAACTTGTT
CCTAGTTGCTGTTCATGAGCTTGGTCATCCCTTGGGTCTTGGCTATTCCCATGATCCAAAGCCCATAATGTTCCCCCCCC
CCCCCAGTTATATTGACCCCAACACATTTCACCTCTTTGCTGATGACATACATGGCATTCAGTCTCTCTATGGAGCCCCA
TAAAATTAGCAACCCTCATCAAATCCTGACAGTACAGACTCAGCTACCTGTGACCCCAATTTTAGTTTTGATCCTGTCAC
TATAGAGGGAGATGAAATCTTTTTCTTTAAAAACAAGTTCTTCTGGTGGAAGCTTTCTGAGAGTCCATAGAACGGTGTTA
GTTTAATTTCTTTCTTATGGCCAATCTTACCATCTGGCATTCAAGCCACTTATGAAATTGGAGCCAGAAATGATGTTTTT
CTTTTTAAAGATGCTAAGTACTGGTTAGTCATCAATTTAAGATCACAATCAAACTATCTCAAGAGCATACATTCTTTGGG
CTTCCCCTACTCTGTGAAAAAAATTGATGGAGCTGTTTTTAACCCACTTCTCTATAAGACCTGCTTCTTTCTAGATAACC
AATACTGGAGGTATGATGAGAAGAGACAATACATAGACCCCAATTATTCCAAATTGATTACCATGTGCTTCCCAGAAATT
GGGCATAAATTGATTCAATCTTCTATTATAACTGACAAGACTATTTCTTCCAGGGGTCTGAGATACTTGAATACGATGTC
CTATCCCATTGTGTCACCAAAAGGCTGAAAAGCAATATCAAGTTTGGT

Alignment

ORF - retro_ecab_153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.87 %
• Parental protein coverage: 71.2 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MIQFAHGAHGDYSPFDGRNGILAHAFGPGPGIGGDTHFDEAEIWTKSYKGT-NLFLVAVHELGHSLGLGH
          .I.FA.GAHG.YSPFD.RNGI.AHAFG.GPGIGGD.HFDEA.IWT.S.K.T.NLFLVAVHELGH.LGLG.
Retrocopy LI*FAPGAHGHYSPFDDRNGIIAHAFGLGPGIGGDAHFDEAKIWTESCKDT<NLFLVAVHELGHPLGLGY

Parental  SHDPKAIMFPTY-SYIDLSTFRLSADDIRGIQSLYGAPEKPRPSSKPDSTDPTVCDPNMSFDAVTTVGDK
          SHDPK.IM.....SYID..TF.L.ADDI.GIQSLYGAP....PSS.PDSTD...CDPN.SFD.VT..GD.
Retrocopy SHDPKPIMXXXXXSYIDPNTFHLFADDIHGIQSLYGAP*N*QPSSNPDSTDSATCDPNFSFDPVTIEGDE

Parental  IFFFKDRFFWRKLPKSPEINVGLISSLWPTLPSGIQAAYEIGARNHVFLFKDDKYWLISNLRQQPNYPRS
          IFFFK..FFW.KL..SP...V.LIS.LWP.LPSGIQA.YEIGARN.VFLFKD.KYWL..NLR.Q.NY..S
Retrocopy IFFFKNKFFWWKLSESP*NGVSLISFLWPILPSGIQATYEIGARNDVFLFKDAKYWLVINLRSQSNYLKS

Parental  IHSLGFPSHVKKIDAAVFNPHFYKTYFFVDNQYWRYNERRQLMDPGYPKQTTTYFPGVGPK-IDGVFYYN
          IHSLGFP..VKKID.AVFNP..YKT.FF.DNQYWRY.E.RQ..DP.Y.K..T..FP..G.K.ID..FYYN
Retrocopy IHSLGFPYSVKKIDGAVFNPLLYKTCFFLDNQYWRYDEKRQYIDPNYSKLITMCFPEIGHK<IDSIFYYN

Parental  RYYYFLQGSNILEYDVLSRRVTKIMKSNTELG
          ...YF.QGS.ILEYDVLS..VTK..KSN...G
Retrocopy *QDYFFQGSEILEYDVLSHCVTKRLKSNIKFG

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	1.18 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	0.00 RPM	0.00 RPM
SRP021940_placental_villous	0.00 RPM	0.05 RPM
SRP021940_synovial_membrane	0.00 RPM	1.02 RPM
SRP021940_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_153 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_153 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008413	6 retrocopies	retro_chof_1424, retro_chof_1611, retro_chof_2207, retro_chof_325, retro_chof_595, retro_chof_645,
Equus caballus	ENSECAG00000019445	1 retrocopy	retro_ecab_153 ,
Loxodonta africana	ENSLAFG00000010062	1 retrocopy	retro_lafr_147,
Macaca mulatta	ENSMMUG00000004250	1 retrocopy	retro_mmul_2325,
Otolemur garnettii	ENSOGAG00000010221	1 retrocopy	retro_ogar_965,