RetrogeneDB ID: retro_ecab_577

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:28580984..28581610(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOOL
• Ensembl ID: ENSECAG00000009229
• Aliases: None
• Description: apolipoprotein O-like [Source:HGNC Symbol;Acc:24009]

Sequence

>retro_ecab_577
CATTTACAAATGAGCTTTGCATCCATCCGTGCTACAACTGGTCATTATATTGGCTGATGCAAGGGTGTGTACGACTTTGT
AAAAAATGGGATGATGGATACAGAACAATTTGGAAAAGATGCGTATGTCTACCTGAAAAATCCACCTCGAGATTTTCTTC
TGAAAATTGGAGTCATTACAGTCTCAGGGTTGGCAGGCTTGGTTTCAGCAAGAAAAGGTTCTAGGTTTAAGAAAATTGCT
TATCCAATGGGGCTGGCCACTTTAGGAGCATCTGCTTGCTACTCAGTTCAGTCGGTAATAATTGCGAAGGTAACTAGAAG
AAAGGCATATGCTACAAGCAGCCAATTTACGAGGCAGTTAAATCATTGCAGACAAAGAACAACAAAAAAGAGCCACTTCC
TGAACCTAAAGAAACAACTAAGCTAGGAAGGTCTGTTGGGATAGAAATACCTGCAAAAATGACTCACAACCTGAAACACT
CAGTGCCTTTGCCAACAGAACTCAGCCCTGAAACAAAGACCGAATCAGAATCCACCTCAGGTGCTACACACTTTATGCCT
GACCCCAAGCTCATGGATCACAGGCAGTCCCACCCAGAAGATGTAGATGTGTACAGCACTAGAAGC

Alignment

ORF - retro_ecab_577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.81 %
• Parental protein coverage: 77.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NLQMSFASIRATTGRYIGWCKGVYDFVKNGIMDTVQFGKDAYIYLKNPPRDFLPKVGVITVSGLAGLVSA
          .LQMSFASIRATTG.YIG.CKGVYDFVKNG.MDT.QFGKDAY.YLKNPPRDFL.K.GVITVSGLAGLVSA
Retrocopy HLQMSFASIRATTGHYIG*CKGVYDFVKNGMMDTEQFGKDAYVYLKNPPRDFLLKIGVITVSGLAGLVSA

Parental  RKGSRFKKIAYPLGLATLGASVCYPVQSVIIAKVTGRKAYATSQQ-IYEAVKSLWTKNNKKESLPEPKEK
          RKGSRFKKIAYP.GLATLGAS.CY.VQSVIIAKVT.RKAYATS.Q.IYEAVKSL.TKNNKKE.LPEPKE.
Retrocopy RKGSRFKKIAYPMGLATLGASACYSVQSVIIAKVTRRKAYATSSQ<IYEAVKSLQTKNNKKEPLPEPKET

Parental  TKLGSPAEIEIPAKTPHDLKHSVPLPTEFSSETKTKLESPSGATQFLPDPKLMDHGQSHPEDADMYSTRS
          TKLG....IEIPAK..H.LKHSVPLPTE.S.ETKT..ES.SGAT.F.PDPKLMDH.QSHPED.D.YSTRS
Retrocopy TKLGRSVGIEIPAKMTHNLKHSVPLPTELSPETKTESESTSGATHFMPDPKLMDHRQSHPEDVDVYSTRS

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	3.07 RPM
SRP021940_cerebellum	0.00 RPM	2.49 RPM
SRP021940_embryo	0.00 RPM	9.64 RPM
SRP021940_placental_villous	0.00 RPM	13.23 RPM
SRP021940_synovial_membrane	0.00 RPM	5.11 RPM
SRP021940_testis	0.00 RPM	1.34 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_577 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_577 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_577 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000829	1 retrocopy	retro_amel_1035,
Canis familiaris	ENSCAFG00000017383	1 retrocopy	retro_cfam_1490,
Callithrix jacchus	ENSCJAG00000008249	2 retrocopies	retro_cjac_1783, retro_cjac_2464,
Dipodomys ordii	ENSDORG00000011045	1 retrocopy	retro_dord_373,
Equus caballus	ENSECAG00000009229	1 retrocopy	retro_ecab_577 ,
Equus caballus	ENSECAG00000013441	1 retrocopy	retro_ecab_145,
Homo sapiens	ENSG00000155008	1 retrocopy	retro_hsap_3253,
Gorilla gorilla	ENSGGOG00000016329	1 retrocopy	retro_ggor_2213,
Loxodonta africana	ENSLAFG00000008844	1 retrocopy	retro_lafr_1035,
Microcebus murinus	ENSMICG00000015844	1 retrocopy	retro_mmur_1511,
Myotis lucifugus	ENSMLUG00000011384	1 retrocopy	retro_mluc_1364,
Macaca mulatta	ENSMMUG00000004335	1 retrocopy	retro_mmul_2045,
Mustela putorius furo	ENSMPUG00000001899	3 retrocopies	retro_mputfur_606, retro_mputfur_734, retro_mputfur_874,
Nomascus leucogenys	ENSNLEG00000002634	1 retrocopy	retro_nleu_1702,
Pongo abelii	ENSPPYG00000020516	1 retrocopy	retro_pabe_2697,
Pan troglodytes	ENSPTRG00000022067	1 retrocopy	retro_ptro_2200,
Sus scrofa	ENSSSCG00000012459	1 retrocopy	retro_sscr_610,
Tursiops truncatus	ENSTTRG00000000429	1 retrocopy	retro_ttru_1337,