RetrogeneDB ID: retro_ecab_87

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 6:65062350..65063634(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004390
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PCED1A
• Ensembl ID: ENSECAG00000016497
• Aliases: None
• Description: PC-esterase domain containing 1A [Source:HGNC Symbol;Acc:16212]

Sequence

>retro_ecab_87
ATGGTCCACCTGCGGGCTTCCGAAGTGCGGCAGCTGCTCCACAACAAGTTCGTGGTCATCCTGGGGGACTCTGTCCACAG
GGCCGTGTACAAGGACCTGGTGCTCCTGCTGCAGAAGGACTGCCTGCTCACGCCCAGCCAGCTCAAGGCCAAGGGGGAGG
AGAGCTTCGAACAGGACATTCTCTTGGAGGGAGGCCAGCTGGGCCCCATGCACAACGGCATCGAGTACCGCGAGGTCCGC
CAGTTCTGCTCCGGCCACCATCTGGTGCGCTTCTACTTCCTCACGCGCGTGTACTCCGACTACCTCAAGGCCATCTTGCA
ACAGCTGCAGTCGGGCGAGCACTTCCCAGACGTGATCATCATGAACTCCTGCCTCTGGGACATCTCCAGGTACGGTGAGC
ACTCGTGGTCGAGCTACCTGGAGAACCTGACGAGGCTGTTTGGGCACCTGGGCCAGATGCTGCCCGAGTCGTGCCTCATG
GTGTGGAACACAGCCATGCCGCTTGGCGACAAACTCTCCGCCGGCTTTCTCCCGCCCGAGCCCCAACCCTGGACCAACGC
CCTGAAATTCAGGGTGGTCGAAGCCAATTTCTACAGCTCTGTGGAGGCCAAGAACCACGGCTTCGACGTGCTGGACTTGC
ATTTCCACTTCCGCCGTGCGCAGCAGCATCACCTGCAGCGAGACGGGGTGCACTGGGACGAGTATGCGCACCGACAGCTC
TCCCAGCTGCTGCTGGCCCACGTGGCCGACGCCTGGGGGGTGGAGCTGCCCCAACGCGACCCAGTGGGCAGGTGGATCAA
GGACGGCCCTGCAAGAGGAGAACGTGCCCAGGGAGCTGAGAGGCAGCCCCTGGCCCGCAGAGGTCAACGGACCTTATCTC
TGCCTGGACCCTTGCCTCCTCGCACGTGCTACCCCCTGCTCTCGCTCCCATCTCCTCGCCCACCCCTGCTCCCACTCCTG
CCCCGACAGCCTTCTCCCATCCGCTTTCACCAACCCATGCCCCAGTTTCTCCTCTGTCCCCAAGATGCCTGTTTGTCCTC
AGACCGTCCGGATCAATTCTCCTTAAGCCATTTCCATTCAGATGGCCCCTTCGAAACTGACTTTATGTTAGGTCCCCAGC
CACCTGTGCCGCCTTTCCCCACACCCCGTTATCATCGGCAGCGGGCCCCTGTGGTTCATAGGGGGTTTCCCCAGTATTCG
CCCCGTGGCCCGTATGGGCCCTGGAGGCAGCCCAGACCTTTCAGGAGAAGGGCCCCAGCCCACCCAAAGCCAAGGTTTCA
ATAG

Alignment

ORF - retro_ecab_87 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.36 %
• Parental protein coverage: 73.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVHFQASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDSLLTAAQLKAKGELSFEQDQLVAGGQLGEL
          MVH..ASEV.QLLHNKFVVILGDS..RAVYKDLVLLLQKD.LLT..QLKAKGE.SFEQD.L..GGQLG..
Retrocopy MVHLRASEVRQLLHNKFVVILGDSVHRAVYKDLVLLLQKDCLLTPSQLKAKGEESFEQDILLEGGQLGPM

Parental  HNGTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEDVLEELTCGP-APDLVIINSCLWDLSRYGRCSMES
          HNG..YREVRQFC..SGHHLVRFYFLTRVYS.YL...L..L..G...PD..I.NSCLWD.SRYG..S..S
Retrocopy HNGIEYREVRQFC--SGHHLVRFYFLTRVYSDYLKAILQQLQSGEHFPDVIIMNSCLWDISRYGEHSWSS

Parental  YRENLERVFVRMDQVLPDSCLLVWNMAMPLGERVTGGFLLPE-QSLAGSLRRDVVEGNFYSATLAGDHFY
          Y.ENL.R.F....Q.LP.SCL.VWN.AMPLG.....GFL.PE.Q.....L...VVE.NFYS...A..H..
Retrocopy YLENLTRLFGHLGQMLPESCLMVWNTAMPLGDKLSAGFLPPEPQPWTNALKFRVVEANFYSSVEAKNHGF

Parental  DVLDLHFHFRHAVQHR-HRDGIHWDQHAHRHLSQLLLTHVADAWGVELPKRDYPPDPWIEDWPEPDHLFQ
          DVLDLHFHFR.A.QH...RDG.HWD..AHR.LSQLLL.HVADAWGVELP.RD.P...WI.D.P......Q
Retrocopy DVLDLHFHFRRAQQHHLQRDGVHWDEYAHRQLSQLLLAHVADAWGVELPQRD-PVGRWIKDGPARGERAQ

Parental  GSQGQPPDFGEQLALPPPPPSPLPPPMPFP-YPLPQPSPP--PLFPPLPQDATFFPGQP
          G...QP.....Q..L..P...PLPP....P...LP.P.PP..PL.P..P....F....P
Retrocopy GAERQPLARRGQRTLSLP--GPLPPRTCYPLLSLPSPRPPLLPLLPRQPSPIRFHQPMP

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	53.48 RPM
SRP021940_cerebellum	0.00 RPM	56.50 RPM
SRP021940_embryo	0.51 RPM	83.80 RPM
SRP021940_placental_villous	1.15 RPM	23.86 RPM
SRP021940_synovial_membrane	1.02 RPM	52.90 RPM
SRP021940_testis	4.41 RPM	34.59 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_87 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_87 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_87 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_182

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003863	1 retrocopy	retro_btau_182,
Cavia porcellus	ENSCPOG00000025475	2 retrocopies	retro_cpor_343, retro_cpor_79,
Equus caballus	ENSECAG00000016497	1 retrocopy	retro_ecab_87 ,
Felis catus	ENSFCAG00000002886	1 retrocopy	retro_fcat_18,
Homo sapiens	ENSG00000132635	2 retrocopies	retro_hsap_2207, retro_hsap_82,
Microcebus murinus	ENSMICG00000016578	2 retrocopies	retro_mmur_163, retro_mmur_278,
Myotis lucifugus	ENSMLUG00000028662	2 retrocopies	retro_mluc_222, retro_mluc_647,
Macaca mulatta	ENSMMUG00000005200	2 retrocopies	retro_mmul_333, retro_mmul_341,
Mus musculus	ENSMUSG00000037773	2 retrocopies	retro_mmus_1001, retro_mmus_332,
Otolemur garnettii	ENSOGAG00000004701	1 retrocopy	retro_ogar_81,
Pongo abelii	ENSPPYG00000010833	2 retrocopies	retro_pabe_192, retro_pabe_2080,
Pan troglodytes	ENSPTRG00000013185	1 retrocopy	retro_ptro_105,
Pteropus vampyrus	ENSPVAG00000006834	1 retrocopy	retro_pvam_9,
Sus scrofa	ENSSSCG00000007168	1 retrocopy	retro_sscr_23,
Ictidomys tridecemlineatus	ENSSTOG00000016356	2 retrocopies	retro_itri_1190, retro_itri_783,
Tursiops truncatus	ENSTTRG00000003464	1 retrocopy	retro_ttru_16,