RetrogeneDB ID: retro_ecab_166

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:62988368..62989283(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK16
• Ensembl ID: ENSECAG00000014093
• Aliases: None
• Description: serine/threonine kinase 16 [Source:HGNC Symbol;Acc:11394]

Sequence

>retro_ecab_166
ATGGGCCACACACTGTGTGTCTGCTCTCGGGGAACTGTCATCATTGACAATAAGCGCTACCTCTTCATCCAGAAACTAGG
GGAGGGTGGGTTCAGCTATGTGGACCTAGTAGGGGGGTTACATGATGGACACTTCTACACCCTGAAGCGAATCCTGTGTC
ACGAGCAGCAGGACCAGGAAGATGCCCAATGAGAAGCAGACATGCATCGCCTCTTCCATCACCCCAACATCCTTCACCTT
GTGGCTTATTGTCTGAAGGAGCGGGGCGCTAAACATGAGGCCTGGCTGCTGCTACCTTTCTTCAAGAGAGATACACTGTG
GACCGAGACAGAATGGCTCAAGGACAAAGGTAACTTCTTGACTGAAGATCAAATCCTTCAGCTGCTGCTGGGTATCTGCA
GAGGACTTGAGGCCATTCACGCCAAGGGTTATGCCTACAGGGACATGAAGCCCACTAATATCTTGCTTGGAGATGAGGGG
CAGCCAGTTTTAATGGACTTGGGTTCCACGAATCAAGCATGCATCCACGTGGAGGGCTCCCTCCAGGCTCTGGCCCTGCA
GGACTGGGCAGCTCAGGGGTGCACCATCTCCTACTGGGCCCTGGAGCTCTTCTCCGTGCAGAGCCACTGTGTCATCGATG
AGGGGACTGATGTCTGGTCCCTAGGCTGCGTGTTATATGCCATGATGTTTGGGGAAGGCCCTTATGACATGGTGTTCCAG
AAGGGTGACAGTGTGGCCCTTGCTGTGCAGAACCAACTGAACATCCGGCAGAGCCCCAGGCATTCTGCAGTGATGTGGCA
GCTGCTGGCCTCGATGATGACTGTGGACCCGCAGCAGCGCCCTCACGTTCCTCTCCTCCTAAGTCAGTTGGAAGCACTGC
AACCCTCAGCTCCAGGCCAGCACACTACCCAAATC

Alignment

ORF - retro_ecab_166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.46 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGHALCVCSRGTVIIDNKRYLFIQKLGEGGFSYVDLVEGLHDGHFYALKRILCHEQQDREDAQREADMHH
          MGH.LCVCSRGTVIIDNKRYLFIQKLGEGGFSYVDLV.GLHDGHFY.LKRILCHEQQD.EDAQ.EADMH.
Retrocopy MGHTLCVCSRGTVIIDNKRYLFIQKLGEGGFSYVDLVGGLHDGHFYTLKRILCHEQQDQEDAQ*EADMHR

Parental  LFHHPNILRLVAYCLKERGAKHEAWLLLPFFKRGTLWTEIERLKDKGNFLTQDQILQLLLGICRGLEAIH
          LFHHPNIL.LVAYCLKERGAKHEAWLLLPFFKR.TLWTE.E.LKDKGNFLT.DQILQLLLGICRGLEAIH
Retrocopy LFHHPNILHLVAYCLKERGAKHEAWLLLPFFKRDTLWTETEWLKDKGNFLTEDQILQLLLGICRGLEAIH

Parental  AKGYAHRDLKPTNILLGDEGQPVLMDLGSMNQACIHVEGSRQALALQDWAAQRCTISYRAPELFSVQSHC
          AKGYA.RD.KPTNILLGDEGQPVLMDLGS.NQACIHVEGS.QALALQDWAAQ.CTISY.A.ELFSVQSHC
Retrocopy AKGYAYRDMKPTNILLGDEGQPVLMDLGSTNQACIHVEGSLQALALQDWAAQGCTISYWALELFSVQSHC

Parental  VIDERTDVWSLGCVLYAMMFGEGPYDMVFQKGDSVALAVQNQLNIPQSPRHSAAMRQLLASMMTVDPQQR
          VIDE.TDVWSLGCVLYAMMFGEGPYDMVFQKGDSVALAVQNQLNI.QSPRHSA.M.QLLASMMTVDPQQR
Retrocopy VIDEGTDVWSLGCVLYAMMFGEGPYDMVFQKGDSVALAVQNQLNIRQSPRHSAVMWQLLASMMTVDPQQR

Parental  PHIPLLLSQLEALQPSAPGQHTTQI
          PH.PLLLSQLEALQPSAPGQHTTQI
Retrocopy PHVPLLLSQLEALQPSAPGQHTTQI

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	12.22 RPM
SRP021940_cerebellum	0.16 RPM	15.27 RPM
SRP021940_embryo	0.13 RPM	22.91 RPM
SRP021940_placental_villous	0.10 RPM	10.78 RPM
SRP021940_synovial_membrane	0.25 RPM	14.30 RPM
SRP021940_testis	0.06 RPM	47.83 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_166 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_166 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_166 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000000152	1 retrocopy	retro_dord_692,
Equus caballus	ENSECAG00000014093	1 retrocopy	retro_ecab_166 ,
Homo sapiens	ENSG00000115661	1 retrocopy	retro_hsap_1334,
Gorilla gorilla	ENSGGOG00000010907	1 retrocopy	retro_ggor_1040,
Macropus eugenii	ENSMEUG00000006422	1 retrocopy	retro_meug_1579,
Myotis lucifugus	ENSMLUG00000008066	1 retrocopy	retro_mluc_1213,
Pongo abelii	ENSPPYG00000013202	1 retrocopy	retro_pabe_1108,
Pan troglodytes	ENSPTRG00000012948	1 retrocopy	retro_ptro_911,
Ictidomys tridecemlineatus	ENSSTOG00000025197	2 retrocopies	retro_itri_1662, retro_itri_602,