RetrogeneDB ID: retro_ecab_347

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 15:33094633..33095245(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC94
• Ensembl ID: ENSECAG00000022785
• Aliases: None
• Description: coiled-coil domain containing 94 [Source:HGNC Symbol;Acc:25518]

Sequence

>retro_ecab_347
TTTGACCAGTCAAAGATCCTCAAGCTCAGGGTCCCCAGGACTGGCACCATGTGGTGCGGTCAACGGCCCCTTCAGCCCGA
CGTGTGAGACCTGAGGAGAATACAGCTACGGGGGAAAGAAATTCGACGCGCAAAGAGAGGGCGCAGAACAGGCCTCCAGG
GACCCGCCCACCTTCCGTTTCCGCTTCCGGTTCTGTTTCCGTACGTCGAGTGCGTGCGCTACCAGGCAGACAGCACCTTC
AAGACAGACCCCGAAGGCACGGACTGCACCGTGGAGCACAGGGCTACAGGGAACTTCCAGGCCGAGAAGCCCCTGGAGCA
GGAGGAGAAGAGGCTGCGGGAGGACGAGGGGCTGAGCAACCCCATGAAAGTTGCTGGAGAGACCAACCCAAAGCCTCAGG
CTGGGATGGAGACTGGAGAACCTGCAGGAGCTCGAGGACCTGAGCCGGCGGAGGCCCCCAGGGACTTTGAGGCCGCACTG
CGGCAGCACCGCCTGCGAGGAGGACGGGCAGGAGCAGGAGGAGGACGAGAGGGAGACGGCGGCCTTAGTGGAAGAAGCTA
GCAAACGAAGACCGCTGGAGACTCCCATTCAGAGGAGGATGCTGCTGCTCCC

Alignment

ORF - retro_ecab_347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55. %
• Parental protein coverage: 64.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  FDPSKIPKLKLPK-DRQYVVRLMAP-FNMRCKTCGEYIY-KGKKFN----ARKETVQNEAYLG--LPIFR
          FD.SKI.KL..P..D...VVR..AP.F...C.T.GEY.Y..GK........R....Q..A.L...LP...
Retrocopy FDQSKILKLRVPR<DWHHVVRSTAP<FSPTCET*GEYSY<RGKEIRRAKRGRRTGLQGPAHLPFPLPVLF

Parental  FYIKCTRCLAEITFKTDPENTDYTMEHGATRNFQAEKLLEEEEKRVQKEREDEELNNPMKV-LENRTKDS
          .Y..C.R..A..TFKTDPE.TD.T.EH.AT.NFQAEK.LE.EEKR....REDE.L.NPMKV.LE..T...
Retrocopy PYVECVRYQADSTFKTDPEGTDCTVEHRATGNFQAEKPLEQEEKRL---REDEGLSNPMKV>LERPTQSL

Parental  KLEMEVLENLQELKDLNQR-QAHVDFEAMLRQHRL-SEEERQKQEQEEDERETAALVEESRKRRLLE-DS
          .L....LENLQEL.DL..R..A..DFEA.LRQHRL..E......E...DERETAALVEE..KRR.LE.DS
Retrocopy RLGWR-LENLQELEDLSRR<EAPRDFEAALRQHRL>EEDGQEQEE---DERETAALVEEASKRRPLE<DS

Parental  DSEEEDAPAP
          .S.EEDA.AP
Retrocopy HS-EEDAAAP

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	0.12 RPM	7.67 RPM
SRP021940_cerebellum	0.00 RPM	19.58 RPM
SRP021940_embryo	0.00 RPM	14.17 RPM
SRP021940_placental_villous	0.10 RPM	8.32 RPM
SRP021940_synovial_membrane	0.11 RPM	11.01 RPM
SRP021940_testis	0.13 RPM	76.80 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_347 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_347 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_347 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000022785	1 retrocopy	retro_ecab_347 ,
Monodelphis domestica	ENSMODG00000000841	1 retrocopy	retro_mdom_496,
Mus musculus	ENSMUSG00000003208	1 retrocopy	retro_mmus_1640,
Otolemur garnettii	ENSOGAG00000001662	1 retrocopy	retro_ogar_168,
Sarcophilus harrisii	ENSSHAG00000010428	1 retrocopy	retro_shar_394,