RetrogeneDB ID: retro_ecab_923

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:24438764..24439280(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL9
• Ensembl ID: ENSECAG00000007545
• Aliases: None
• Description: myosin, light chain 9, regulatory [Source:HGNC Symbol;Acc:15754]

Sequence

>retro_ecab_923
ATGTCCAGCAAACCGGCCAAGGCCAAGACCACTAAGAAGCGGCCACAGCGGGCCACATCCAATGTCTTCGCGATGTTTGA
CCAGTCCCAGATCCAGGAGTTTAAGGAGGCCTTCAACATGATGGACCAGAACTGAGATGGCTTCATTGGCAAGGAGGACT
TGCATGACACGCTGGCCTCGATGGGGAAGGACCCCACGGACGAGTACCTGGAGGGCATGATGAGCGAGGTCCCGGGGCCC
ATCAACTTCACCATGTTCCTCACCATGTTTGAGGAGAAGCTGAACGGCACAGACCCCGAGGACGTGACCCGCAACGCCTT
CACCTGCTTCGACGAGGAGGCCTCAGGCTTCATCCATGAGGACCACCTTCAGGAGTTGCTCACCACCATGGGCGACCGCT
TCACAGACGAGGAGGTGGACGAGATGTACCGCGAGGCACCCATTGATAAGAAAGGCAACTTTAACTATGTGGAGTTCACC
CGTATCCTCAAACATGGTGCCAAGGACAAAGACGAC

Alignment

ORF - retro_ecab_923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.6 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSKRAKAKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMIDQNRDGFIDKEDLHDMLASMGKNPTDEYL
          MSSK.AKAKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNM.DQN.DGFI.KEDLHD.LASMGK.PTDEYL
Retrocopy MSSKPAKAKTTKKRPQRATSNVFAMFDQSQIQEFKEAFNMMDQN*DGFIGKEDLHDTLASMGKDPTDEYL

Parental  EGMMSEAPGPINFTMFLTMFGEKLNGTDPEDVIRNAFACFDEEASGFIHEDHLRELLTTMGDRFTDEEVD
          EGMMSE.PGPINFTMFLTMF.EKLNGTDPEDV.RNAF.CFDEEASGFIHEDHL.ELLTTMGDRFTDEEVD
Retrocopy EGMMSEVPGPINFTMFLTMFEEKLNGTDPEDVTRNAFTCFDEEASGFIHEDHLQELLTTMGDRFTDEEVD

Parental  EMYREAPIDKKGNFNYVEFTRILKHGAKDKDD
          EMYREAPIDKKGNFNYVEFTRILKHGAKDKDD
Retrocopy EMYREAPIDKKGNFNYVEFTRILKHGAKDKDD

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	8.97 RPM
SRP021940_cerebellum	0.16 RPM	21.86 RPM
SRP021940_embryo	0.46 RPM	109.63 RPM
SRP021940_placental_villous	0.91 RPM	240.03 RPM
SRP021940_synovial_membrane	1.10 RPM	164.00 RPM
SRP021940_testis	0.26 RPM	36.58 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_923 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_923 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_923 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008540	3 retrocopies	retro_cfam_1384, retro_cfam_2066, retro_cfam_2071,
Callithrix jacchus	ENSCJAG00000012890	4 retrocopies	retro_cjac_3193, retro_cjac_3195, retro_cjac_3743, retro_cjac_637,
Equus caballus	ENSECAG00000007545	1 retrocopy	retro_ecab_923 ,
Homo sapiens	ENSG00000101335	1 retrocopy	retro_hsap_956,
Gorilla gorilla	ENSGGOG00000024477	1 retrocopy	retro_ggor_770,
Myotis lucifugus	ENSMLUG00000000207	2 retrocopies	retro_mluc_2534, retro_mluc_327,
Nomascus leucogenys	ENSNLEG00000006109	1 retrocopy	retro_nleu_2460,
Pongo abelii	ENSPPYG00000010971	1 retrocopy	retro_pabe_972,
Pan troglodytes	ENSPTRG00000013458	1 retrocopy	retro_ptro_662,