RetrogeneDB ID: retro_ecab_271

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 12:6868711..6869763(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000002481
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACTB
• Ensembl ID: ENSECAG00000015935
• Aliases: None
• Description: actin, cytoplasmic 1 [Source:RefSeq peptide;Acc:NP_001075307]

Sequence

>retro_ecab_271
GACGCCCCCTGCACCGTCTTCCGCTCCATTGTGGGGCACCCCCGGCACCAGGGCGTGATGGTGGGCATGGGCCAGAAGGA
CTCGTACGTGGGCGACGAGGCCCAGAGCAAGAGGGGCCTCCTGACCCCCAAGTACCCCATCGAGCACGGCATCGTCACCA
ACTGGGACGGCATGGAGAAGATCTGGCACCACACCTTCTACAACGAGCTGTGCGTGGCCCCCGAGGAGCACCCCGTGCTG
CTGACTGAGGCCCCCCTGAACCCCAAGGCCAACCGCGAGAAGATGACCCAGATCATGTTCGAGACCTTCAACACCCTGGC
CATGTATGTGGCCATCCAGGCCGTGCTGTCCCTGTACGCCTCTGGCTGCACCACTGGCATCGTGATGGACTCCGGTGACG
GGGTCACCCACACTGTGCCCATCTACGAGGGGTACGCCCTCCCCCACACCATCCTGCGTCTGGACCTGGCTGGCCGGGAC
CTGACGGACTACCTCATGAAGATCCTCACGGAGCGTGGCTACAGCTTCACCACCACGGCCGAGCGGGAAATCGTGCGTGA
CATTAAGGAGAGGCTCTGCTATGTCGCCCTGGACTTCGAGCAGGAGATGGCCACCGTGGCCTCCAGCTCTTCCCTGGAGA
AGAGCTACGAGCTGCCCCACGGCCAGGTCATCACCATCGGCAACAAGCGGTTCCGGGCCCCCGAGGCCCTCTTCCACTCT
CCTTCCTGGGAATGGAATCCAGTGGCATCCACGAAACTGCCTTCAACTCTATCATGAAGTGTGACGTCGACATCCATAAG
GACCTGTATGCCAACACAGTGCTGTCAGGTGGGACCACCCTGTACCCAGGCATCGCCGACAGGATGCAGAAGGAGATCAC
AGCCCTGGCTCCCAGCACGATGAAGATCAAGATCATCGCGCCCCCCGAGCGCAAGTACTCCGTATGGATTGGCGGCTCCA
TTCTGGCCTCATCGTCCACCTTCCAGCAGATGTGGATCACCAAGCAGGAGTACAACGAGTCCGGCCCCTCCATAGTCCAC
CGCAAATGCTTC

Alignment

ORF - retro_ecab_271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.18 %
• Parental protein coverage: 96.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNEL
          DAP..VF.SIVG.PRHQGVMVGMGQKDSYVGDEAQSKRG.LT.KYPIEHGIVTNWD.MEKIWHHTFYNEL
Retrocopy DAPCTVFRSIVGHPRHQGVMVGMGQKDSYVGDEAQSKRGLLTPKYPIEHGIVTNWDGMEKIWHHTFYNEL

Parental  RVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVP
          .VAPEEHPVLLTEAPLNPKANREKMTQIMFETFNT.AMYVAIQAVLSLYASG.TTGIVMDSGDGVTHTVP
Retrocopy CVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTLAMYVAIQAVLSLYASGCTTGIVMDSGDGVTHTVP

Parental  IYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSS
          IYEGYALPH.ILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKE.LCYVALDFEQEMAT.ASSS
Retrocopy IYEGYALPHTILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKERLCYVALDFEQEMATVASSS

Parental  SLEKSYELPDGQVITIGNERFRAPEALFQP-SFLGMESSGIHETTFNSIMKCDVDIRKDLYANTVLSGGT
          SLEKSYELP.GQVITIGN.RFRAPEALF...SFLGMESSGIHET.FNSIMKCDVDI.KDLYANTVLSGGT
Retrocopy SLEKSYELPHGQVITIGNKRFRAPEALFHS<SFLGMESSGIHETAFNSIMKCDVDIHKDLYANTVLSGGT

Parental  TMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRK
          T.YPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS.STFQQMWI.KQEY.ESGPSIVHRK
Retrocopy TLYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASSSTFQQMWITKQEYNESGPSIVHRK

Parental  CF
          CF
Retrocopy CF

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	0.59 RPM	299.28 RPM
SRP021940_cerebellum	1.66 RPM	493.67 RPM
SRP021940_embryo	5.93 RPM	1174.91 RPM
SRP021940_placental_villous	21.89 RPM	1350.86 RPM
SRP021940_synovial_membrane	5.11 RPM	1075.57 RPM
SRP021940_testis	2.43 RPM	313.64 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_271 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_271 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
Anas platyrhynchos	ENSAPLG00000010147	1 retrocopy	retro_apla_2,
Canis familiaris	ENSCAFG00000016020	3 retrocopies	retro_cfam_120, retro_cfam_260, retro_cfam_934,
Callithrix jacchus	ENSCJAG00000000008	2 retrocopies	retro_cjac_243, retro_cjac_56,
Dipodomys ordii	ENSDORG00000010079	1 retrocopy	retro_dord_11,
Equus caballus	ENSECAG00000015935	2 retrocopies	retro_ecab_271 , retro_ecab_994,
Equus caballus	ENSECAG00000018600	1 retrocopy	retro_ecab_98,
Felis catus	ENSFCAG00000006788	1 retrocopy	retro_fcat_1613,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pan troglodytes	ENSPTRG00000018890	27 retrocopies	retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,