RetrogeneDB ID: retro_ecab_33

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:144481370..144481937(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000002176
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000024877
• Aliases: None
• Description: None

Sequence

>retro_ecab_33
ATGAATACAAGAATGGGCTATGGTAGCATGGTGAATTCCAGACAAGCCCGAGAATTCCATACAGCTGGAGAAAGAGGCCC
AACTCCTCAGACAGTCTTGGAAGCAGAACTGATAGAACTTGGGGAAAGTGATGAAGTAGTTGACCTCACCTGTGAATCTC
TAGAACCTGCAGTGATTGACCTAACTCACCAGGACTGTGTTGTGATTACTGAAGAAAGGAGGCGGCCAAGGGGAAACACA
AGGTCACTCCAAGGCCAAACTGGCAGCTGTGTGGTGAGCAGTGATAAGGAATTGATGAGGGACAGAGATGTATATGTGAC
CCATAGTGCCTACCATAATGCCCTGGAAGAAGAAACTTTAAGTTGCACACTACCTGGTTATATCCAGTGTCGAATTTGTA
TGGATGGGTACTCGGAGATTGAATTGAGTAGACGGCACATCTACTCTACAGACTGTGGCCACATCTTCTGTAGTCAGTGC
CTCTGTACTTCCCTTAAATATACTAAAACTTGCCCAGTTTGTTTGAAAAAAATTGGCTGCCGTCAGTACCATCGTATTTA
TTTATGA

Alignment

ORF - retro_ecab_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTRKRRGGTVNSRQAQK--RTREAASTPEMALEAEPIELVESAGDEIVDLTCESLEPVVVDLTHNDSVV
          M.TR...G..VNSRQA.......E...TP...LEAE.IEL.ES..DE.VDLTCESLEP.V.DLTH.D.VV
Retrocopy MNTRMGYGSMVNSRQAREFHTAGERGPTPQTVLEAELIELGES--DEVVDLTCESLEPAVIDLTHQDCVV

Parental  IVDERRRPRRNARRLRQDHADSCVVSSDDEELSRDRDVYVTTHTPRNTREEAATGLRPSGTVSCPICMDG
          I..ERRRPR.N.R.L.Q....SCVVSSD..EL.RDRDVYVT.....N..EE........G...C.ICMDG
Retrocopy ITEERRRPRGNTRSL-QGQTGSCVVSSD-KELMRDRDVYVTHSAYHNALEEETLSCTLPGYIQCRICMDG

Parental  YSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI
          YSEI....R.I.ST.CGH.FCSQCL..SLK...TCP.C.KKI....YH.IY.
Retrocopy YSEIELSRRHIYSTDCGHIFCSQCLCTSLKYTKTCPVCLKKIGCRQYHRIYL

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	1.53 RPM	12.16 RPM
SRP021940_cerebellum	1.61 RPM	24.41 RPM
SRP021940_embryo	0.31 RPM	32.63 RPM
SRP021940_placental_villous	6.11 RPM	24.73 RPM
SRP021940_synovial_membrane	4.69 RPM	28.17 RPM
SRP021940_testis	1.15 RPM	54.10 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_33 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_33 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_33 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1144
Pongo abelii	retro_pabe_1240
Sus scrofa	retro_sscr_181
Canis familiaris	retro_cfam_25

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014366	1 retrocopy	retro_amel_77,
Canis familiaris	ENSCAFG00000014856	1 retrocopy	retro_cfam_25,
Dipodomys ordii	ENSDORG00000006675	2 retrocopies	retro_dord_347, retro_dord_411,
Equus caballus	ENSECAG00000024877	1 retrocopy	retro_ecab_33 ,
Echinops telfairi	ENSETEG00000001683	3 retrocopies	retro_etel_469, retro_etel_626, retro_etel_627,
Felis catus	ENSFCAG00000004051	1 retrocopy	retro_fcat_897,
Homo sapiens	ENSG00000063978	1 retrocopy	retro_hsap_319,
Gorilla gorilla	ENSGGOG00000015149	2 retrocopies	retro_ggor_1144, retro_ggor_345,
Loxodonta africana	ENSLAFG00000007382	1 retrocopy	retro_lafr_44,
Microcebus murinus	ENSMICG00000001767	1 retrocopy	retro_mmur_1265,
Myotis lucifugus	ENSMLUG00000005969	1 retrocopy	retro_mluc_1640,
Mus musculus	ENSMUSG00000029110	1 retrocopy	retro_mmus_522,
Nomascus leucogenys	ENSNLEG00000000160	2 retrocopies	retro_nleu_1713, retro_nleu_37,
Oryctolagus cuniculus	ENSOCUG00000004998	2 retrocopies	retro_ocun_1566, retro_ocun_162,
Otolemur garnettii	ENSOGAG00000010776	1 retrocopy	retro_ogar_2121,
Ochotona princeps	ENSOPRG00000004317	3 retrocopies	retro_opri_112, retro_opri_783, retro_opri_863,
Procavia capensis	ENSPCAG00000004528	1 retrocopy	retro_pcap_208,
Pongo abelii	ENSPPYG00000025865	2 retrocopies	retro_pabe_1240, retro_pabe_36,
Pteropus vampyrus	ENSPVAG00000017017	1 retrocopy	retro_pvam_167,
Sus scrofa	ENSSSCG00000008690	1 retrocopy	retro_sscr_181,
Ictidomys tridecemlineatus	ENSSTOG00000011101	2 retrocopies	retro_itri_1108, retro_itri_171,
Tarsius syrichta	ENSTSYG00000011244	1 retrocopy	retro_tsyr_1606,