RetrogeneDB ID: retro_ecab_510

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 2:13006808..13007382(-)
• Located in intron of: ENSECAG00000017621

Retrocopy information

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

Parental gene information

• Parental gene symbol: GM2A
• Ensembl ID: ENSECAG00000020587
• Aliases: None
• Description: ganglioside GM2 activator [Source:RefSeq peptide;Acc:NP_001075381]

Sequence

>retro_ecab_510
AGACCCTCGATGCAGGCTCCATTCCTGATCGCCGTGGGCTTGCTTCTTGCTGGCCCTGCGGCTCCTGTAAGCATCCTCCT
AGACAGCTCAGTAGATTTTCCTGGGTAACTGTGATGAGGGGAAGGATCCTGTGGTGATCAAAACCCTGACTGTGGAACCT
GACCCCATTGCTGTTCCTGGAAACGTGACTGTCAGTGCCGAGGTAAAGACCACTGTCCCCTTCATTGCTCCTCAGAAGGT
GGAAATAACTCTGGATAAGGAAGTGGCCAGTGTATGGGTCAAAATCCCGTGTATGGAACAAATCGGTAGCTGTACATTTG
ACAATGCCTATGATATGCTTGACACTTAAGACTCCCCCTGGGCAATCCTGCCCAGAGCCCCTGCACACCTATGGGCTTCC
TTGTCGCTGTCCCTTCAAAGAAGCCACCTACTCATTGCCCAAGAGTACTTTCCCCTCCCCAACCTGGAGCTGCCCAGCTG
GCTCAACAACAGGAACTACCGCATCCAGAGCGTCCTGAGCGGCAGTGGGACTCGTCTGGGCTGTATCAAGATCTCCACCT
CTCTAAAGGGCAAA

Alignment

ORF - retro_ecab_510 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.04 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RPSMQAPFLIALGLLLAGPAAPVSVLSE-RLRSFSW-DNCDEGKDPMVLKSLTLEPDPIAVPGNVTVSAE
          RPSMQAPFLIA.GLLLAGPAAPVS.L....L..FSW..NCDEGKDP.V.K.LT.EPDPIAVPGNVTVSAE
Retrocopy RPSMQAPFLIAVGLLLAGPAAPVSILLD<QLSRFSW<GNCDEGKDPVVIKTLTVEPDPIAVPGNVTVSAE

Parental  VKTTVALSAPQKVELTVEKEVAGVWVKIPCVDQIGSCTFDNACDILDA-LTPPGQPCPEPLHTFGLPCHC
          VKTTV...APQKVE.T..KEVA.VWVKIPC..QIGSCTFDNA.D.LD...TPPGQ.CPEPLHT.GLPC.C
Retrocopy VKTTVPFIAPQKVEITLDKEVASVWVKIPCMEQIGSCTFDNAYDMLDT>KTPPGQSCPEPLHTYGLPCRC

Parental  PFKEGTYSLPKST-FPLPDLELPSWLSNGNYRVQSILSSGGKRLGCVKITASLKAK
          PFKE.TYSLPKST.FPLP.LELPSWL.N.NYR.QS.LS..G.RLGC.KI..SLK.K
Retrocopy PFKEATYSLPKST<FPLPNLELPSWLNNRNYRIQSVLSGSGTRLGCIKISTSLKGK

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	11.16 RPM
SRP021940_cerebellum	0.05 RPM	23.47 RPM
SRP021940_embryo	0.03 RPM	11.15 RPM
SRP021940_placental_villous	0.34 RPM	3507.01 RPM
SRP021940_synovial_membrane	0.03 RPM	27.89 RPM
SRP021940_testis	0.00 RPM	48.21 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_510 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_510 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_510 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000020587	1 retrocopy	retro_ecab_510 ,
Homo sapiens	ENSG00000196743	2 retrocopies	retro_hsap_264, retro_hsap_2715,
Gorilla gorilla	ENSGGOG00000015302	2 retrocopies	retro_ggor_1891, retro_ggor_313,
Macropus eugenii	ENSMEUG00000010421	1 retrocopy	retro_meug_1818,
Microcebus murinus	ENSMICG00000000690	1 retrocopy	retro_mmur_518,
Myotis lucifugus	ENSMLUG00000003215	1 retrocopy	retro_mluc_920,
Macaca mulatta	ENSMMUG00000022869	1 retrocopy	retro_mmul_454,
Nomascus leucogenys	ENSNLEG00000010966	1 retrocopy	retro_nleu_866,
Oryctolagus cuniculus	ENSOCUG00000015837	1 retrocopy	retro_ocun_704,
Ochotona princeps	ENSOPRG00000006171	1 retrocopy	retro_opri_1169,
Pongo abelii	ENSPPYG00000015962	1 retrocopy	retro_pabe_403,
Pan troglodytes	ENSPTRG00000017431	2 retrocopies	retro_ptro_1834, retro_ptro_221,
Ictidomys tridecemlineatus	ENSSTOG00000028500	1 retrocopy	retro_itri_759,
Tursiops truncatus	ENSTTRG00000000503	1 retrocopy	retro_ttru_488,