RetrogeneDB ID: retro_ecab_120

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:34200314..34201173(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCB1
• Ensembl ID: ENSECAG00000007797
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 [Source:HGNC Symbol;Acc:11103]

Sequence

>retro_ecab_120
GAAGCCTCTGAGGTGGAAGAGATAGTAGACAGCAAGGATGAGAAATACAAGGTATGTGTCCATCAGCATGGAGCCCCCAA
ACTACTTCAGGGAACAGAAAACCAAGAGGCACAGCCAGTGGGTGCCCATCTTGCCCAACATTTCTCACCATCTGGATACT
GTGCCATGCTCTACTACCATTAACAGCAGCCTCACAGGCTGGGACAAGAAGAGAACGTTCCCTCTCTGCTTTGATGATCA
CGACCCACCTGTGATCCATGACAACATGACCCAGCCTGTGGTGTTAGTCCCCATCTCACTGGAAATGGAGACCAAGGGGC
AGAAGGTGCCAGACCCTTTACCTGAAACAAGAATGAGAAGCCAATGACCCCTGAGACATCTTCGGAAATCTTCTGTGACC
ACCTAGATTTGAACTTGCAGACATTGTTTCAGCTATCACCTCTGCCATCACACAGAAGATCAAGTCCTACCCACCCACAG
AATCCTGGAGGACCAGTTGGAGCAGTGCGTCATCATTAAGCTGAACAACCCTTTGGGAAATGTTGCCGTAGTGGATCAGT
AGAGTGGGACATGTCAGAGAAGGAGAACTCCCTAGAGAACCTTGCCCTGAAGCTGTCTTCAGAGCTGGGGCTGGGCATGG
AGGAGGTTGTCACCACCGCTGCATACAACATTCAGGGACAGTCTAGCTGGCATAGGAAGACCTACACCTTCAGGGAGAAT
GCCCTGCCTATGGTGAAGATTGCCATCGGAACACAGGCGGTGCTAATTAGTGGTGCCCACTACTGGAGACATTGATGATG
CCAAGATGAAAAATAAGATCTGTGACCAGGACAAGAACACGAGGCATTTGAGATATCTC

Alignment

ORF - retro_ecab_120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.08 %
• Parental protein coverage: 78.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  KASEVEEILDGNDEKYKA-VSISTEPPTYLREQKAKRNSQWVPTLPNSSHHLDAVPCSTTINRNRMGRDK
          .ASEVEEI.D..DEKYK..VSIS.EPP.Y.REQK.KR.SQWVP.LPN.SHHLD.VPCSTTIN....G.DK
Retrocopy EASEVEEIVDSKDEKYKV>VSISMEPPNYFREQKTKRHSQWVPILPNISHHLDTVPCSTTINSSLTGWDK

Parental  KRTFPLCFDDHDPAVIHENASQPEVLVPIRLDMEIDGQKLRD-AFTWNMNEKLMTPEMFSEILCDDLDLN
          KRTFPLCFDDHDP.VIH.N..QP.VLVPI.L.ME..GQK..D..FT.N.NEK.MTPE..SEI.CD.LDLN
Retrocopy KRTFPLCFDDHDPPVIHDNMTQPVVLVPISLEMETKGQKVPD<PFT*NKNEKPMTPETSSEIFCDHLDLN

Parental  PLT-FVPAIASAIRQQIESY-HLDAVSRDKGQKRVCWPLNIHVGNISLVDQ-FEWDMSEKENSPEKFALK
          ..T..V.AI.SAI.Q.I.SY........D.....V...LN...GN...VDQ..EWDMSEKENS.E..ALK
Retrocopy LQT<IVSAITSAITQKIKSY<PTHRILEDQLEQCVIIKLNNPLGNVAVVDQ<VEWDMSEKENSLENLALK

Parental  LCSELGLG-GEFVTTIAYSIRGQLSWHQKTYAFSENPLPTVEIAI-RNTGDADQWCPLLETL-TDAEMEK
          L.SELGLG..E.VTT.AY.I.GQ.SWH.KTY.F.EN.LP.V.IAI.RNTG.A..WCPLLETL..DA.M..
Retrocopy LSSELGLGMEEVVTTAAYNIQGQSSWHRKTYTFRENALPMVKIAI<RNTGGAN*WCPLLETL<DDAKMKN

Parental  KIRDQDRNTRRMRRL
          KI.DQD.NTR..R.L
Retrocopy KICDQDKNTRHLRYL

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	20.01 RPM
SRP021940_cerebellum	0.00 RPM	81.69 RPM
SRP021940_embryo	0.03 RPM	147.20 RPM
SRP021940_placental_villous	0.00 RPM	43.44 RPM
SRP021940_synovial_membrane	0.00 RPM	48.43 RPM
SRP021940_testis	0.00 RPM	57.93 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_120 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_120 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_120 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000007797	2 retrocopies	retro_ecab_120 , retro_ecab_121,