RetrogeneDB ID: retro_ecab_660

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 26:30987780..30988480(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM106C
• Ensembl ID: ENSECAG00000020351
• Aliases: None
• Description: transmembrane protein 106C [Source:HGNC Symbol;Acc:28775]

Sequence

>retro_ecab_660
AAGAGAGAAGATGACAGGGAGGATTTGCAGCCTGAACAAGAGCAGGAAGGAGCCATTGCCCAGTTCCCACATGTGGAGTA
CATGTGGTGAGATAGCATTACAGTCTCATGTGTCAAGGGACAGGTTACCTTCCAACAGAGGAAGTGAATGAGTAGGTGGG
TTCAATCCCACACAGAGATCAGAGATTGTGCCCTCAGAGAACTAAGCAGTGTGTCCTCCTGTCCACCCTGTTCTGTCTCC
TGGCATCTGAGTGGGGGTATTCTTCCTGCTTCTGCATTCAGTCCTTGCGGATGATTATAGCATCAAAGTAGTGAAAGTCA
CGTTTAATAAGCAGAACTCCCCTGTAATCCTTGCCAACATGGCCACCCTGAAAATCAGGAACTCCAACTTCTACCCTATG
GGAGGAGCCAGCCTGTCCAGTCATGTTCAGTACATGAACACAATGTTTGGGACATATACGACAACTAATGCTTCCTTCAT
TTGACCTTGGAGTGAGCAACTGGTGAATTTTACCACAAAGGCTGAGATGGGAGTACCATTTTCCTATGTGTGCTTTTTCT
GCATAGTACCTGATGTCCTGGACCACAACATAGTGATCTTCATGTGAACTTCCGTGAAGCTTTCATTCATTGGCCACATG
ACCTGGAGATCCTTGGAGACACATCACTATGTGGATTGTGGAGCAAATTCCATAGCTGTT

Alignment

ORF - retro_ecab_660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.92 %
• Parental protein coverage: 93.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKKDDREDFLAEREQEEAIAQFPYVEFTGRDSITC-LTCQGTGYIPTEQVNELVALIPHSDQRLRPQRTK
          ...DDRED...E.EQE.AIAQFP.VE....DSIT..L.CQGTGY.PTE.VNE.V..IPH.DQRL.PQRTK
Retrocopy KREDDREDLQPEQEQEGAIAQFPHVEYMW*DSITV<LMCQGTGYLPTEEVNE*VGSIPHRDQRLCPQRTK

Parental  QYVLLSVLLCLLASG-LVVFFLFPHSVLVDDDGIKVVKVTFNKQDSLVILAITATLKIRNSNFYSVAVTS
          Q.VLLS.L.CLLAS....VFFL..HSVL.DD..IKVVKVTFNKQ.S.VILA..ATLKIRNSNFY.....S
Retrocopy QCVLLSTLFCLLASE<VGVFFLLLHSVLADDYSIKVVKVTFNKQNSPVILANMATLKIRNSNFYPMGGAS

Parental  LSTQVQYMNTVVGSYVTANVSLIPPRSEHLVNFTVKAEMGGPYSYVYFFCTLPDILIHNIVIFMRTSVKI
          LS..VQYMNT..G.Y.T.N.S.I.P.SE.LVNFT.KAEMG.P.SYV.FFC..PD.L.HNIVIFM.TSVK.
Retrocopy LSSHVQYMNTMFGTYTTTNASFI*PWSEQLVNFTTKAEMGVPFSYVCFFCIVPDVLDHNIVIFM*TSVKL

Parental  SYIGHVTQSSLETHHYVDCGANSTAV
          S.IGH.T..SLETHHYVDCGANS.AV
Retrocopy SFIGHMTWRSLETHHYVDCGANSIAV

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	0.00 RPM
SRP021940_cerebellum	0.00 RPM	0.16 RPM
SRP021940_embryo	0.03 RPM	32.61 RPM
SRP021940_placental_villous	0.00 RPM	23.77 RPM
SRP021940_synovial_membrane	0.05 RPM	18.53 RPM
SRP021940_testis	0.00 RPM	24.62 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_660 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_660 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_660 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008335	1 retrocopy	retro_cpor_1124,
Equus caballus	ENSECAG00000020351	1 retrocopy	retro_ecab_660 ,
Echinops telfairi	ENSETEG00000010370	1 retrocopy	retro_etel_173,
Myotis lucifugus	ENSMLUG00000017734	1 retrocopy	retro_mluc_1096,
Pteropus vampyrus	ENSPVAG00000014352	1 retrocopy	retro_pvam_562,
Sus scrofa	ENSSSCG00000028397	1 retrocopy	retro_sscr_473,
Tarsius syrichta	ENSTSYG00000001184	1 retrocopy	retro_tsyr_1263,