RetrogeneDB ID: retro_ecab_991

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 8:38123361..38123959(-)
• Located in intron of: ENSECAG00000005343

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP1B
• Ensembl ID: ENSECAG00000018625
• Aliases: None
• Description: charged multivesicular body protein 1B [Source:HGNC Symbol;Acc:24287]

Sequence

>retro_ecab_991
ATGTCCAACATGGAGAAACACCTGTTCAAACCTGAAGTTCGCGGCCAAAGAACTGAGCAGGAGTGCCAAAAAATGCGACA
AGGAGGAAAAGGCCGAAAAGGCCAAAATTAAAAAGGCCATTCAGAAGGGCAACATGGAAGTTGCGAGGATTCACGCCGAA
AATGCCATTCGCCAGAAGAACCAGGCGGTGAATTTCTTGAGAATGAGTGCGCGGGTTGATGCTGTGGCTGCCAGAGTCCA
GACGGCGGTGACGATGGGCAAGGTGACCAAGTCGATGGCCGGTGTGGTTAAGTCGATGGATGCGACGCTGAAGACCATGA
ATCTGGAGAAGATCTCTGCCTTAATGGACAAATTCGAGCACCAGTTTGAGACGCTGGATGTCCAGACGCAGCAAATGGAA
GACACGATGAGCAGCACGACGACGCTGACCACTCCCCAGAACCAAGTGGATATGCTGCTCCAGGAAATGGCAGACGAGGC
CGGCCTAGACCTCAACATGGAGCTGCCGCAGGGGCAGACCGGCTCCGTGGCTACGAGCGTGGCTTCGGCCGAGCAGGATG
AACTATCCCAGAGACTGGCCCGCCTGCGGGATCAAGTG

Alignment

ORF - retro_ecab_991 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSNMEKHLF-NLKFAAKELNRNAKKCDKEEKAEKAKIKKAIQKGNTEVARIHAENAIRQKNQAINFLRMS
          MSNMEKHLF.NLKFAAKEL.R.A.................IQKGN.EVARIHAENAIRQKNQA.NFLRMS
Retrocopy MSNMEKHLF>NLKFAAKELSRSAXXXXXXXXXXXXXXXXXIQKGNMEVARIHAENAIRQKNQAVNFLRMS

Parental  ARVDAVAARVQTAVTMGKVTKSMAGVVKSMDATLRSMNLEKISALMDKFEHQFETLDVQTQQMEDTMSST
          ARVDAVAARVQTAVTMGKVTKSMAGVVKSMDATL..MNLEKISALMDKFEHQFETLDVQTQQMEDTMSST
Retrocopy ARVDAVAARVQTAVTMGKVTKSMAGVVKSMDATLKTMNLEKISALMDKFEHQFETLDVQTQQMEDTMSST

Parental  TTLTTPQNQVDMLLQEMADEAGLDLNMELPQGQTGSVGTSVASTEQDELSQRLARLRDQV
          TTLTTPQNQVDMLLQEMADEAGLDLNMELPQGQTGSV.TSVAS.EQDELSQRLARLRDQV
Retrocopy TTLTTPQNQVDMLLQEMADEAGLDLNMELPQGQTGSVATSVASAEQDELSQRLARLRDQV

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	16.53 RPM	0.65 RPM
SRP021940_cerebellum	21.81 RPM	1.30 RPM
SRP021940_embryo	28.72 RPM	3.09 RPM
SRP021940_placental_villous	30.12 RPM	11.35 RPM
SRP021940_synovial_membrane	17.90 RPM	2.06 RPM
SRP021940_testis	12.09 RPM	1.28 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_991 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_991 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_991 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_75
Pan troglodytes	retro_ptro_1278
Gorilla gorilla	retro_ggor_1368
Pongo abelii	retro_pabe_1581
Callithrix jacchus	retro_cjac_1147
Oryctolagus cuniculus	retro_ocun_1508
Rattus norvegicus	retro_rnor_1361
Canis familiaris	retro_cfam_1866

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000026660	1 retrocopy	retro_cpor_1434,
Equus caballus	ENSECAG00000018625	1 retrocopy	retro_ecab_991 ,
Gorilla gorilla	ENSGGOG00000025604	1 retrocopy	retro_ggor_1368,
Loxodonta africana	ENSLAFG00000026457	2 retrocopies	retro_lafr_214, retro_lafr_826,
Macropus eugenii	ENSMEUG00000015250	2 retrocopies	retro_meug_1196, retro_meug_205,
Myotis lucifugus	ENSMLUG00000024811	3 retrocopies	retro_mluc_1161, retro_mluc_1344, retro_mluc_673,
Monodelphis domestica	ENSMODG00000004273	2 retrocopies	retro_mdom_1444, retro_mdom_154,
Mus musculus	ENSMUSG00000031242	1 retrocopy	retro_mmus_1735,
Ochotona princeps	ENSOPRG00000018556	1 retrocopy	retro_opri_577,
Pongo abelii	ENSPPYG00000020505	1 retrocopy	retro_pabe_1581,
Pteropus vampyrus	ENSPVAG00000001416	2 retrocopies	retro_pvam_208, retro_pvam_59,
Rattus norvegicus	ENSRNOG00000002323	2 retrocopies	retro_rnor_1361, retro_rnor_623,
Sarcophilus harrisii	ENSSHAG00000016903	2 retrocopies	retro_shar_776, retro_shar_778,
Tarsius syrichta	ENSTSYG00000011727	1 retrocopy	retro_tsyr_1611,
Tursiops truncatus	ENSTTRG00000008066	2 retrocopies	retro_ttru_1002, retro_ttru_235,
Vicugna pacos	ENSVPAG00000000854	2 retrocopies	retro_vpac_112, retro_vpac_422,