RetrogeneDB ID: retro_ecab_798

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 4:95205214..95206117(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCP1
• Ensembl ID: ENSECAG00000017953
• Aliases: None
• Description: t-complex 1 [Source:HGNC Symbol;Acc:11655]

Sequence

>retro_ecab_798
ACAGACCCTGAAAAACTGCATCAGATTAGACAGAGAAAATCAGATATCACCAAGGGGCAAATCCAGAAGATTCTGGAAAC
TGATGTCAATGTTATTCTAACCACTGATGGAATTGACAATATGTGTCTGAACCATTTTGCAGAGACTGGCACTATAGCAG
TTAGAAGAATTTTAAAAAGGGACCTTAAATGCATTGGTAAAGATTCTGGAGTAATTACTCTGTCAACTCTGGCCAGTTTG
GAAGGCAAAGAAACTTTTGAAGCTTTAATGTTAAGACAAGCAGAAGAGGTGGTACAGGAGAGAATTCATGATGATGAAGT
GATCTTCATCAAAAACACTAAAGCCCATACATCTGCATCAGCTATCTTTTGTGAAGTGAATGATTTCATGTGTGGTGAGA
TGGAGTGCTCTTTACAAGATGTTCTTTGTGTGGTGAAGAGAGTTTTGGCATCAAAAATCTGTGGTTCCAGGTAGGGGTGC
TGTAGAAGCAGCCTTGTCCATGTATCTTGAAAACTATGCAGTCAGCACAGGGTCCCCGGAATAGCTTGCTATTGCAGAGT
TGCAAGCTCTCTTCTTGCTATTCCTAATGCATTGGCAGTTTATGCTTCCCGAGACTCCATAGATCTGGCTGCAAAGTTAA
GAGCTTTTCATAATGAGGTTCAAGTTAACCAAGAATGCAAAAATCTAAAATGGATTAGTCTTGATTTGGTCAATGGAAAA
CCTTGAGACAACAAACAAGCAGAGGTGTGTGAACCAATCATAGTTAAAATTAAGAGTTCGAAATTTGCAGTGGAGGTTGC
AATTACTGTTCTTCAAATTGATATTATTAAATTACACCTAGAAAGAAAAAAAGATGATAAGTATGGAGGTTATGAAGATA
CTGTTCACTAGGGAGCCCTTAAT

Alignment

ORF - retro_ecab_798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.01 %
• Parental protein coverage: 53.94 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TDPEKLDQIRQRESDITKERIQKILATGANVILTTGGIDDMCLKYFVETGAMAVRRVLKRDLKRIAKASG
          TDPEKL.QIRQR.SDITK..IQKIL.T..NVILTT.GID.MCL..F.ETG..AVRR.LKRDLK.I.K.SG
Retrocopy TDPEKLHQIRQRKSDITKGQIQKILETDVNVILTTDGIDNMCLNHFAETGTIAVRRILKRDLKCIGKDSG

Parental  ATILSTLANLEGEETFEASMLGQAEEVVQERICDDELILIKNTKARTSASVILRGANDFMCDEMERSLHD
          ...LSTLA.LEG.ETFEA.ML.QAEEVVQERI.DDE.I.IKNTKA.TSAS.I....NDFMC.EME.SL.D
Retrocopy VITLSTLASLEGKETFEALMLRQAEEVVQERIHDDEVIFIKNTKAHTSASAIFCEVNDFMCGEMECSLQD

Parental  ALCVVKRVLES-KSVVPGGGAVEAALSIYLENYATSMGSREQLAIAEF-ARSLLVIPNTLAVNAAQDSTD
          .LCVVKRVL.S.KSVVPG.GAVEAALS.YLENYA.S.GS.E.LAIAE..A.SLL.IPN.LAV.A..DS.D
Retrocopy VLCVVKRVLAS>KSVVPGRGAVEAALSMYLENYAVSTGSPE*LAIAEL<ASSLLAIPNALAVYASRDSID

Parental  LVAKLRAFHNEAQVNPERKNLKWIGLDLVNGKPRDNKQAGVFEPTIVKVKSLKFATEAAITILRIDDLIK
          L.AKLRAFHNE.QVN.E.KNLKWI.LDLVNGKP.DNKQA.V.EP.IVK.KS.KFA.E.AIT.L.I.D.IK
Retrocopy LAAKLRAFHNEVQVNQECKNLKWISLDLVNGKP*DNKQAEVCEPIIVKIKSSKFAVEVAITVLQI-DIIK

Parental  LHPE-SKDDKHGGYEDAVHSGALD
          LH.E..KDDK.GGYED.VH.GAL.
Retrocopy LHLERKKDDKYGGYEDTVH*GALN

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	47.34 RPM
SRP021940_cerebellum	0.00 RPM	102.05 RPM
SRP021940_embryo	0.00 RPM	126.92 RPM
SRP021940_placental_villous	0.00 RPM	75.73 RPM
SRP021940_synovial_membrane	0.00 RPM	50.98 RPM
SRP021940_testis	0.13 RPM	376.37 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_798 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_798 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_798 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015405	1 retrocopy	retro_amel_828,
Callithrix jacchus	ENSCJAG00000011792	2 retrocopies	retro_cjac_1867, retro_cjac_2193,
Equus caballus	ENSECAG00000017953	1 retrocopy	retro_ecab_798 ,
Homo sapiens	ENSG00000120438	1 retrocopy	retro_hsap_3722,
Gorilla gorilla	ENSGGOG00000014063	1 retrocopy	retro_ggor_2514,
Microcebus murinus	ENSMICG00000007998	1 retrocopy	retro_mmur_795,
Macaca mulatta	ENSMMUG00000012846	1 retrocopy	retro_mmul_1696,
Oryctolagus cuniculus	ENSOCUG00000013847	1 retrocopy	retro_ocun_1577,
Pongo abelii	ENSPPYG00000017146	1 retrocopy	retro_pabe_3135,
Pan troglodytes	ENSPTRG00000018760	1 retrocopy	retro_ptro_2617,
Pteropus vampyrus	ENSPVAG00000005316	1 retrocopy	retro_pvam_522,
Rattus norvegicus	ENSRNOG00000014160	1 retrocopy	retro_rnor_2091,
Sorex araneus	ENSSARG00000002463	1 retrocopy	retro_sara_624,
Sarcophilus harrisii	ENSSHAG00000015128	1 retrocopy	retro_shar_830,
Ictidomys tridecemlineatus	ENSSTOG00000005572	1 retrocopy	retro_itri_1274,