RetrogeneDB ID: retro_ecab_566

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 21:26260160..26261019(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC11
• Ensembl ID: ENSECAG00000010219
• Aliases: None
• Description: coiled-coil domain containing 11 [Source:HGNC Symbol;Acc:26530]

Sequence

>retro_ecab_566
TTTGTGACTGGAAAGCTAGACAACAATTCAGGGAGTGCTGTGAGGAGCTCCGCGTTGAGCTGCTTGCATTCATCAGAAAG
TGTGTGAGGAACAGAAAGCACAGACAGAACTTAGAGAGGAACTGAAGAGGCAGAAACTGGTGAAAGAAGAGACACTCTAG
AACTTCCAGAGGAAGACCGATGAGCCAAGGAAAAGTGAGAAGCCCAAGAGGCGAGGAGTCAGAAAGAGCCAGTGCAGAAC
ACACACCTGGGATAGGATGCCTACGTCACCAACATCAAAGCACAAAGGCCGGTGGTCCAGTGGCCGAGGGAAGAGGCAGC
TCACCTTGTGGCAGATGACAACACAAGGCTAAACTTGAGAACGAAAAGGATAAGCTGAAGAAACAGAAGACAAAGCAAGA
AATTAGAACCCTTTTGCAAAAAGCCCTCCAACAGAAGGTAAAGCATATTCAGCAGGAATACAAAACAGAGCAAGACTTGA
ACTTGAAGCTCGTGCAAAGGGTCCTTCGAGACTTACAGGAAGAGGCTGATAAAAAAGAAGCAAAAAGGAAGACATGGGAA
GAAAACAGAAGATATCTCATGAGCATGTGACACAGCAATGTAAGGAAGAGAAAGCTCAGGAGAAAGAAGTGGACAAAATA
ATAGAAGAGGAGAAGGAAAAGAAGTTTGCTGAGAAAGACAGGCAGCTGAAATTTGAAAAGAAGGCGCGGAAACAGCGCTT
GTGAATGAGGTCACGTGTAAAGAAAAATTAAAGAAATGTTGCAAGAAAAGCAAAAGAACAGGAAGAATGTGCTATGAAAC
AGGATCACACAAATGAAGGTCCTAAAGAACTTGACAGCGAAGAAGAGAACTTCGTAAGA

Alignment

ORF - retro_ecab_566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.25 %
• Parental protein coverage: 66.51 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  FVAEKLD-QQFRERCEELRVEL-SCIHEKKVCEERKAQVAFNEELKRQKLVEEQMF-SKLWEEDRLAKEK
          FV..KLD.QQFRE.CEELRVEL..CIH.K.VCEE.KAQ....EELKRQKLV.E......L.EEDR.AKEK
Retrocopy FVTGKLD<QQFRECCEELRVEL<ACIHQK-VCEEQKAQTELREELKRQKLVKEETL<LELPEEDR*AKEK

Parental  REAEEARRQKELVENTRLGLNAQITSIKAQRQAEQRLKEEEARLVEKDKAQV-KLENEQDKLKTQKTKRE
          .EA.EAR.QKE.V.NT.LG..A..T.IKAQR...Q...EE.A.LV..D.....KLENE.DKLK.QKTK.E
Retrocopy *EAQEARSQKEPVQNTHLG*DAYVTNIKAQRPVVQWPREEAAHLVADDNTRL<KLENEKDKLKKQKTKQE

Parental  IKTALQKALQEKIEKIQQGYREEQDLDMKLVQMALQDLQEEADKKKQKR-EEMVREQKIYRQYLAQRREE
          I.T.LQKALQ.K...IQQ.Y..EQDL..KLVQ..L.DLQEEADKK..KR.E.M.R.QKI......Q...E
Retrocopy IRTLLQKALQQKVKHIQQEYKTEQDLNLKLVQRVLRDLQEEADKKEAKR<EDMGRKQKISHEHVTQQCKE

Parental  DKAQEKELDRILEEEEKKKLAEKDKELRLEKEARKQLVNEVMCTRKLQVQEKLQRKAKEQEERAMEQERI
          .KAQEKE.D.I.EEE..KK.AE..K...L..E.........M..R.........RKAKEQEE.AM.Q...
Retrocopy EKAQEKEVDKIIEEEKEKKFAE--KDRQLKFEKKARKQRL*MRSRVKKN*RNVARKAKEQEECAMKQDHT

Parental  NEGLKELNREEKENFAR
          NEG.KEL..EE.ENF.R
Retrocopy NEGPKELDSEE-ENFVR

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	0.35 RPM
SRP021940_cerebellum	0.00 RPM	2.96 RPM
SRP021940_embryo	0.00 RPM	1.64 RPM
SRP021940_placental_villous	0.00 RPM	0.72 RPM
SRP021940_synovial_membrane	0.00 RPM	0.96 RPM
SRP021940_testis	0.00 RPM	11.77 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_566 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_566 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_1869

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002660	1 retrocopy	retro_btau_906,
Callithrix jacchus	ENSCJAG00000004928	1 retrocopy	retro_cjac_1869,
Equus caballus	ENSECAG00000010219	1 retrocopy	retro_ecab_566 ,