RetrogeneDB ID: retro_ecab_98

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:15166313..15167444(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000004482
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ACTB
• Ensembl ID: ENSECAG00000018600
• Aliases: None
• Description: Actin, cytoplasmic 1, N-terminally processed [Source:UniProtKB/TrEMBL;Acc:F7A5E3]

Sequence

>retro_ecab_98
ATGACTGATGAGGAGCTGTCTGCCTTGGTGGTGGACAATGGGTCAGGGATGTGCAAGGCAGGCTTTGGTGGTGACGATGC
CCCCCGAGCTGTGTTCCCCTCCATGGTGGGGCGTCCCCGGCACCAGGGGGTCATGGTAGGCATGGGCCAGAAGGACTGCT
ACGTGGGAGACGAGGCCCAGAGCAAGAGAGGCATACTGACCCTGAAGTATCCCATTGAACATGGAGTGGTCACCAACTGG
GACGATATGGAGAAGATCTGGCACCACACTTTCTACAATGAGCTCCGCGTGGCACCAGATGAGCATCCCATCCTCCTCAC
CGAGGCACCCCTCAACCCCAAGATCAACCGGGAAAAGATGACCCAGATCATGTTCGAGGCCTTCAATACACCTGCCATGT
ATGTGGCTATCCAGGCTGTACTGTCCCTCTATGCCTCTGGAAGGACCACAGGCATCGTGATGGATTCTGGGGATGGGGTC
ACGCACACTGTACCCATCTATGAAGGTTATGCCCTGCCCCACGCCATTCTACGTTTAGATCTGGCTGGCAGAGACCTCAC
TGATTACCTCATGAAGATCCTGACAGAACGAGGCTACAACTTCACCACCACAGCTGAGCGGGAGATTGTTCGCGATGTCA
AAGAGAAGCTGTGCTATGTGGCCCTGGACTTTGAGCAAGAGATGGTCAGTGCTGCCACATCCTCCTCACTTGAAAGAAGC
TATGAGCTCCCTGATGGGCAGGTGATCACGATTGGGAATGAACGCTTTCGATGCCCTGAAGCCATTTTCCAGCCTTCTTT
TCTGGGCATTGAGTCCAACGGGATCCACGAGATGACCTTCAACTCAATCATGAAGTGTGACGTGGATATTCGCAAGGATC
TATATGCCAACACGGTGCTATCTGGAGGTAGCACTATGTACCCAGGCATTGCCGACCGGATGCAGAAGGAAATCGTAACC
CTGGCACCAGGCTCCATGAAAATCAAGATCATAGCTCCCCCAGAGCGGAAGTATTCCGTCTGGATAGGAGGCTCCATTCT
GGCCAGCCTGTCCACATTCCAGCAGATGTGGATCAGTAAGCAGGAATATGATGAGGCTGGTCCTCCCATCGTTCATAGAA
AATGTTTCTGA

Alignment

ORF - retro_ecab_98 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.25 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPI
          .EE..ALV.DNGSGMCKAGF.GDDAPRAVFPS.VGRPRHQGVMVGMGQKD.YVGDEAQSKRGILTLKYPI
Retrocopy DEELSALVVDNGSGMCKAGFGGDDAPRAVFPSMVGRPRHQGVMVGMGQKDCYVGDEAQSKRGILTLKYPI

Parental  EHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLS
          EHG.VTNWDDMEKIWHHTFYNELRVAP.EHP.LLTEAPLNPK.NREKMTQIMFE.FNTPAMYVAIQAVLS
Retrocopy EHGVVTNWDDMEKIWHHTFYNELRVAPDEHPILLTEAPLNPKINREKMTQIMFEAFNTPAMYVAIQAVLS

Parental  LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRD
          LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGY.FTTTAEREIVRD
Retrocopy LYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYNFTTTAEREIVRD

Parental  IKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNS
          .KEKLCYVALDFEQEM..AA.SSSLE.SYELPDGQVITIGNERFRCPEA.FQPSFLG.ES.GIHE.TFNS
Retrocopy VKEKLCYVALDFEQEMVSAATSSSLERSYELPDGQVITIGNERFRCPEAIFQPSFLGIESNGIHEMTFNS

Parental  IMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLST
          IMKCDVDIRKDLYANTVLSGG.TMYPGIADRMQKEI..LAP..MKIKIIAPPERKYSVWIGGSILASLST
Retrocopy IMKCDVDIRKDLYANTVLSGGSTMYPGIADRMQKEIVTLAPGSMKIKIIAPPERKYSVWIGGSILASLST

Parental  FQQMWISKQEYDESGPSIVHRKCF
          FQQMWISKQEYDE.GP.IVHRKCF
Retrocopy FQQMWISKQEYDEAGPPIVHRKCF

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	1578.04 RPM
SRP021940_cerebellum	0.00 RPM	1785.49 RPM
SRP021940_embryo	0.26 RPM	3537.37 RPM
SRP021940_placental_villous	0.29 RPM	3022.15 RPM
SRP021940_synovial_membrane	0.16 RPM	2152.76 RPM
SRP021940_testis	0.06 RPM	2537.71 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_98 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_98 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_98 has 10 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_38
Pan troglodytes	retro_ptro_53
Gorilla gorilla	retro_ggor_1297
Pongo abelii	retro_pabe_86
Callithrix jacchus	retro_cjac_243
Mus musculus	retro_mmus_283
Rattus norvegicus	retro_rnor_351
Oryctolagus cuniculus	retro_ocun_38
Bos taurus	retro_btau_903
Canis familiaris	retro_cfam_934

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca	ENSAMEG00000016015	1 retrocopy	retro_amel_929,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus	ENSCPOG00000012101	1 retrocopy	retro_cpor_361,
Equus caballus	ENSECAG00000015935	2 retrocopies	retro_ecab_271, retro_ecab_994,
Equus caballus	ENSECAG00000018600	1 retrocopy	retro_ecab_98 ,
Felis catus	ENSFCAG00000026434	2 retrocopies	retro_fcat_257, retro_fcat_377,
Homo sapiens	ENSG00000184009	10 retrocopies	retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus	ENSGALG00000028749	1 retrocopy	retro_ggal_6,
Gorilla gorilla	ENSGGOG00000014043	6 retrocopies	retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Monodelphis domestica	ENSMODG00000002647	3 retrocopies	retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furo	ENSMPUG00000011610	1 retrocopy	retro_mputfur_279,
Mus musculus	ENSMUSG00000062825	7 retrocopies	retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pongo abelii	ENSPPYG00000008735	11 retrocopies	retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621, retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pelodiscus sinensis	ENSPSIG00000002102	2 retrocopies	retro_psin_25, retro_psin_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Sus scrofa	ENSSSCG00000028355	1 retrocopy	retro_sscr_389,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,