RetrogeneDB ID: retro_ecab_931

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:54763963..54765145(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000005999
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: eca-mir-492-1
• Ensembl ID: ENSECAG00000014086
• Aliases: None
• Description: eca-mir-492-1 [Source:miRBase;Acc:MI0012676]

Sequence

>retro_ecab_931
ATGACTTCCTACAGCTATCGCCAGTCCTCGGCCACCTCGTCCTTCGGGGGCCTGGGCAGTGGCTCCCTGCGCTTCGGGGC
CGGAGGCACCTTCCGCGCGCCCAGCATCCACGGGGGCTCGGGCGGCCGCGGCGTGTCGGTGTCCTCTGCCCGCTTCGTGA
CCTCGTCCTCCTCCGGGAGCTACGGCGGTGGCTATGCGGGCACCCTGGCCGGGTCCGACGGGCTGCCGGCGGGCAACGAG
AAGGAGACCATGCAGAACCTCAACGACCGCCTGGCCTCCTACCTGGACAAGGTGCGCGCCCTGGAGCAGGCCAACGGCGA
CCTGGAGGTGAAGATCCGCGACTGGTACCTGAAGCAGGGGCCCGGGCCCGCCCGCGACTACAGCCACTACTTCAAGACCA
TCGAGGAGCTGCGGGACAAGATTCTTGGGGCCACCATTGAGAACTCCAAGATTGTTCTGCAGATCGACAATGCCCGTCTG
GCTGCAGATGATTTCCGAACCAAGTTCGAGACTGAGCAGGCTCTGCGCTTGAGTGTGGAGGCCGACATCAATGGCCTGCG
CAGGGTGCTAGACGAGCTGACCCTGGCCAGGACTGACCTGGAGATGCAGATTGAAGGCCTGAAGGAGGAGCTGGCCTACC
TGAAGAAGAACCACGAGGAGGAAATCAGTGTCTTGAGGGGCCAGGTGGGTGGCCAGGTCACTGTGGAGGTGGATTCCGCT
CCAGGCATTGACCTAGCCAAGATCCTGAGCGACATGAGAAGCCAATATGAGGTCATGGCTGAGAAGAACAGGAAGGATGC
TGAAGCCTGGTTCACCACCAAGACTGAGGAGCTGAACCGGGAGGTCGCTGGCCACACGGAGCAGCTGCAGATTAACAAGA
CGGAGATCACCGACCTGCGGCGCACCCTCCAGGGCCTGGAGATCGAGCTGCAGTCTCAGCTCAGCATGAAAGCCGCCCTG
GAAGGCACGCTGGCGGAAACGGAGGCTCGCTTCGGAGCTCAGCTGGCACAGATCCAGGCGCTGATCAGTAGCATCGAAGC
CCAGCTGAGTGACGTGCGTGCTGACACCGAGCGGCAGAACCAGGAGTACCAGCTGCTCCTGGACGTCAAGACTCGGCTGG
AGCAGGAGATCGCCACCTACCGAAGCCTGCTGGAGGCCCAGGACGTCACCCATCAAATCGTG

Alignment

ORF - retro_ecab_931 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTSYSYRQSSATSSFGGLGSGSLRFGAGGNFRAPSIHGGSGGRGVSVSSARFVTSSSSGSYGGGYAGTLA
          MTSYSYRQSSATSSFGGLGSGSLRFGAGG.FRAPSIHGGSGGRGVSVSSARFVTSSSSGSYGGGYAGTLA
Retrocopy MTSYSYRQSSATSSFGGLGSGSLRFGAGGTFRAPSIHGGSGGRGVSVSSARFVTSSSSGSYGGGYAGTLA

Parental  GSDGLPAGNEKETMQNLNDRLASYLDKVRALEQANGDLEVKIRDWYLKQGPGPARDYSHYFKTIEELRDK
          GSDGLPAGNEKETMQNLNDRLASYLDKVRALEQANGDLEVKIRDWYLKQGPGPARDYSHYFKTIEELRDK
Retrocopy GSDGLPAGNEKETMQNLNDRLASYLDKVRALEQANGDLEVKIRDWYLKQGPGPARDYSHYFKTIEELRDK

Parental  ILGATIENSKIVLQIDNARLAADDFRTKFETEQALRLSVEADINGLRRVLDELTLARTDLEMQIEGLKEE
          ILGATIENSKIVLQIDNARLAADDFRTKFETEQALRLSVEADINGLRRVLDELTLARTDLEMQIEGLKEE
Retrocopy ILGATIENSKIVLQIDNARLAADDFRTKFETEQALRLSVEADINGLRRVLDELTLARTDLEMQIEGLKEE

Parental  LAYLKKNHEEEISVLRGQVGGQVTVEVDSAPGIDLAKILSDMRSQYEVMAEKNRKDAEAWFTTKTEELNR
          LAYLKKNHEEEISVLRGQVGGQVTVEVDSAPGIDLAKILSDMRSQYEVMAEKNRKDAEAWFTTKTEELNR
Retrocopy LAYLKKNHEEEISVLRGQVGGQVTVEVDSAPGIDLAKILSDMRSQYEVMAEKNRKDAEAWFTTKTEELNR

Parental  EVAGHTEQLQINKTEITDLRRTLQGLEIELQSQLSMKAALEGTLAETEARFGAQLAQIQALISSIEAQLS
          EVAGHTEQLQINKTEITDLRRTLQGLEIELQSQLSMKAALEGTLAETEARFGAQLAQIQALISSIEAQLS
Retrocopy EVAGHTEQLQINKTEITDLRRTLQGLEIELQSQLSMKAALEGTLAETEARFGAQLAQIQALISSIEAQLS

Parental  DVRADTERQNQEYQLLLDVKTRLEQEIATYRSLLEAQDVTHQIV
          DVRADTERQNQEYQLLLDVKTRLEQEIATYRSLLEAQDVTHQIV
Retrocopy DVRADTERQNQEYQLLLDVKTRLEQEIATYRSLLEAQDVTHQIV

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.00 RPM
SRP021940_embryo	3.89 RPM	3.99 RPM
SRP021940_placental_villous	81.02 RPM	15.06 RPM
SRP021940_synovial_membrane	0.03 RPM	0.08 RPM
SRP021940_testis	0.00 RPM	0.51 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_931 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_931 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_931 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000029756	9 retrocopies	retro_cjac_1151, retro_cjac_1812, retro_cjac_2347, retro_cjac_2646, retro_cjac_3108, retro_cjac_3198, retro_cjac_3237, retro_cjac_3358, retro_cjac_633,
Equus caballus	ENSECAG00000014086	2 retrocopies	retro_ecab_76, retro_ecab_931 ,
Echinops telfairi	ENSETEG00000007881	6 retrocopies	retro_etel_1217, retro_etel_1319, retro_etel_191, retro_etel_480, retro_etel_685, retro_etel_95,
Homo sapiens	ENSG00000171345	3 retrocopies	retro_hsap_3486, retro_hsap_585, retro_hsap_959,
Gorilla gorilla	ENSGGOG00000016901	3 retrocopies	retro_ggor_2352, retro_ggor_518, retro_ggor_773,
Macropus eugenii	ENSMEUG00000016158	3 retrocopies	retro_meug_1860, retro_meug_403, retro_meug_826,
Macaca mulatta	ENSMMUG00000018653	4 retrocopies	retro_mmul_1770, retro_mmul_717, retro_mmul_774, retro_mmul_790,
Nomascus leucogenys	ENSNLEG00000010787	3 retrocopies	retro_nleu_1609, retro_nleu_2204, retro_nleu_800,
Oryctolagus cuniculus	ENSOCUG00000016132	1 retrocopy	retro_ocun_1884,
Otolemur garnettii	ENSOGAG00000024306	1 retrocopy	retro_ogar_1301,
Ochotona princeps	ENSOPRG00000007908	2 retrocopies	retro_opri_337, retro_opri_673,
Pongo abelii	ENSPPYG00000008416	3 retrocopies	retro_pabe_2880, retro_pabe_603, retro_pabe_820,
Pan troglodytes	ENSPTRG00000009168	3 retrocopies	retro_ptro_2074, retro_ptro_2359, retro_ptro_430,
Ictidomys tridecemlineatus	ENSSTOG00000014403	2 retrocopies	retro_itri_1514, retro_itri_697,