RetrogeneDB ID: retro_ecab_138

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:98867223..98867583(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMTOR3
• Ensembl ID: ENSECAG00000013569
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 3 [Source:HGNC Symbol;Acc:15606]

Sequence

>retro_ecab_138
AAGGACCTAACGTGATTCCTGTGTCAAAAACAACTGCGTGTGGAAGGGTTCCAGGCTACTGCTGTGTCAGATGGGGACGG
AGTGGGGTTATCACCGTGGCCAATGCAAGCGCTCCAGATCACGCTTTGAGACCCAGTTTCTTACCTGCTTTTGTCCTCGC
AACAGACCAGGTAGTAAGCTTGGACTTTCAAAAAACAGAAGTATTATCTGTTCCTTTAACACCTAGCAGGTGGTTCCATT
TAAACATTTGCCCTTGGTGAGCAGTTTCACGGCCAGCAGCAAAGCCAATGCAGCACTGTCAGCCGAGAAAAGGAACGTGC
TCCACTATTTGAAGACTTGAGACAAGCCGTGGAAGTTTCT

Alignment

ORF - retro_ecab_138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.6 %
• Parental protein coverage: 98.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QDLKRFLYKKLPSVEGLHAIVVSDRDGVP-VIKVANDNAPEHALRPGFLSTFALATDQ-GSKLGLSKNKS
          .DL..FL..K...VEG..A..VSD.DGV..VI.VAN..AP.HALRP.FL..F.LATDQ.GSKLGLSKN.S
Retrocopy KDLT*FLCQKQLRVEGFQATAVSDGDGVG<VITVANASAPDHALRPSFLPAFVLATDQ<GSKLGLSKNRS

Parental  IICYYNTYQVVQFNRLPLVVSFIASSNANTGLI-VSLEKELAPLFEELRQVVEVS
          IIC..NT.QVV.F..LPL.VS....S........VS.EKE.APLFE.LRQ.VEVS
Retrocopy IICSFNT*QVVPFKHLPL-VSSFTASSKANAAL<VSREKERAPLFEDLRQAVEVS

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	1.95 RPM
SRP021940_cerebellum	0.00 RPM	4.05 RPM
SRP021940_embryo	0.13 RPM	5.06 RPM
SRP021940_placental_villous	0.00 RPM	6.64 RPM
SRP021940_synovial_membrane	0.03 RPM	4.61 RPM
SRP021940_testis	0.51 RPM	8.57 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_138 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_138 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_138 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000995	4 retrocopies	retro_amel_1266, retro_amel_1278, retro_amel_1833, retro_amel_610,
Choloepus hoffmanni	ENSCHOG00000013153	7 retrocopies	retro_chof_1167, retro_chof_1236, retro_chof_1266, retro_chof_1536, retro_chof_166, retro_chof_1929, retro_chof_955,
Callithrix jacchus	ENSCJAG00000015196	4 retrocopies	retro_cjac_1149, retro_cjac_1821, retro_cjac_2581, retro_cjac_2786,
Cavia porcellus	ENSCPOG00000013304	2 retrocopies	retro_cpor_112, retro_cpor_208,
Dasypus novemcinctus	ENSDNOG00000025421	14 retrocopies	retro_dnov_1057, retro_dnov_118, retro_dnov_1190, retro_dnov_1332, retro_dnov_137, retro_dnov_2003, retro_dnov_2213, retro_dnov_2597, retro_dnov_2665, retro_dnov_487, retro_dnov_522, retro_dnov_626, retro_dnov_938, retro_dnov_939,
Dipodomys ordii	ENSDORG00000015501	5 retrocopies	retro_dord_328, retro_dord_379, retro_dord_546, retro_dord_756, retro_dord_771,
Equus caballus	ENSECAG00000013569	1 retrocopy	retro_ecab_138 ,
Homo sapiens	ENSG00000109270	2 retrocopies	retro_hsap_1190, retro_hsap_3374,
Gorilla gorilla	ENSGGOG00000001132	2 retrocopies	retro_ggor_2283, retro_ggor_928,
Loxodonta africana	ENSLAFG00000015740	1 retrocopy	retro_lafr_480,
Myotis lucifugus	ENSMLUG00000006786	2 retrocopies	retro_mluc_2415, retro_mluc_445,
Macaca mulatta	ENSMMUG00000006830	1 retrocopy	retro_mmul_2104,
Monodelphis domestica	ENSMODG00000020688	3 retrocopies	retro_mdom_1133, retro_mdom_455, retro_mdom_907,
Mus musculus	ENSMUSG00000091512	1 retrocopy	retro_mmus_167,
Nomascus leucogenys	ENSNLEG00000013684	2 retrocopies	retro_nleu_1936, retro_nleu_965,
Pongo abelii	ENSPPYG00000014955	3 retrocopies	retro_pabe_1268, retro_pabe_2772, retro_pabe_991,
Pan troglodytes	ENSPTRG00000016310	1 retrocopy	retro_ptro_2294,
Pteropus vampyrus	ENSPVAG00000017674	1 retrocopy	retro_pvam_1378,