RetrogeneDB ID: retro_ecab_220

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:58649189..58649460(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000012046
• Aliases: None
• Description: None

Sequence

>retro_ecab_220
GCTGAACGGATCGAGAAGATCCGAATCGTTGACAAATACAGGACTGGTTACAGTGCCTCTCTCAGGAAAATGGTGAAGAA
AATTGAGCTTGGCCTGCACACCAAGTACACTTGCTCCTTCTGTGGCAAAACCAAAACGGAGAGATGAGCTGTGGGGCTCT
GGCACTGCAATTCTGCGTGAAACAGCAGCTGGAGGGGCCTGGACCTACCACGCCACTTCTGCCGTCTCAGCAAAGTCAGC
CATCAGAGGACCAAAGGAACCGAAAGAGAAG

Alignment

ORF - retro_ecab_220 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 98.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKRRAVGIWHCGS-CMK-TVAGGAW
          A.R..K..IV.KY.T.Y.ASLRKMVKKIE...H.KYTCSFCGKTK..R.AVG.WHC.S.C.K.T.AGGAW
Retrocopy AERIEKIRIVDKYRTGYSASLRKMVKKIELGLHTKYTCSFCGKTKTER*AVGLWHCNS<CVK<TAAGGAW

Parental  TYNTTSAVTVKSAIRRLKELKDQ
          TY..TSAV..KSAIR..KE.K..
Retrocopy TYHATSAVSAKSAIRGPKEPKEK

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	721.05 RPM
SRP021940_cerebellum	0.00 RPM	396.92 RPM
SRP021940_embryo	0.03 RPM	399.91 RPM
SRP021940_placental_villous	0.05 RPM	333.70 RPM
SRP021940_synovial_membrane	0.00 RPM	544.29 RPM
SRP021940_testis	0.00 RPM	352.52 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_220 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_220 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_220 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003377	24 retrocopies	retro_amel_109, retro_amel_1170, retro_amel_1197, retro_amel_1204, retro_amel_1248, retro_amel_1310, retro_amel_1349, retro_amel_1534, retro_amel_1597, retro_amel_1724, retro_amel_1815, retro_amel_1910, retro_amel_1929, retro_amel_248, retro_amel_424, retro_amel_428, retro_amel_475, retro_amel_482, retro_amel_606, retro_amel_737, retro_amel_809, retro_amel_83, retro_amel_920, retro_amel_942,
Callithrix jacchus	ENSCJAG00000012417	7 retrocopies	retro_cjac_1060, retro_cjac_1514, retro_cjac_159, retro_cjac_237, retro_cjac_3178, retro_cjac_335, retro_cjac_888,
Equus caballus	ENSECAG00000012046	6 retrocopies	retro_ecab_220 , retro_ecab_48, retro_ecab_552, retro_ecab_735, retro_ecab_741, retro_ecab_803,
Latimeria chalumnae	ENSLACG00000011578	1 retrocopy	retro_lcha_71,
Loxodonta africana	ENSLAFG00000006849	5 retrocopies	retro_lafr_1010, retro_lafr_1015, retro_lafr_109, retro_lafr_987, retro_lafr_991,
Macropus eugenii	ENSMEUG00000004680	23 retrocopies	retro_meug_1094, retro_meug_111, retro_meug_1120, retro_meug_1289, retro_meug_1302, retro_meug_1399, retro_meug_1600, retro_meug_1705, retro_meug_2021, retro_meug_2061, retro_meug_2143, retro_meug_2173, retro_meug_24, retro_meug_290, retro_meug_458, retro_meug_463, retro_meug_496, retro_meug_502, retro_meug_571, retro_meug_691, retro_meug_813, retro_meug_814, retro_meug_83,
Myotis lucifugus	ENSMLUG00000000762	1 retrocopy	retro_mluc_208,
Petromyzon marinus	ENSPMAG00000000001	1 retrocopy	retro_pmar_11,