RetrogeneDB ID: retro_ogar_1270

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873540.1:25424707..25425963(-)
• Located in intron of: ENSOGAG00000031476

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRFBP1
• Ensembl ID: ENSOGAG00000032423
• Aliases: None
• Description: serum response factor binding protein 1 [Source:HGNC Symbol;Acc:26333]

Sequence

>retro_ogar_1270
CTCAATAACGAGGTCATGAAGAGAAAAGTAGTGAAGAGGATACGAGTTTTGGTTTTCCGAAAACTTGTCAGAATTGTTAA
CAGACTGAAGTCAAAAAAGGGTACTGAAGATGCACTGTTACAAAACCAAAGACGAGCACAACGATTACTTGAAGAGATCC
ATGCCATGAAGGAATTAAAACCTATCTAGTGACTAAATCTGCTCTTGGTGAAGATATCAACTTTGAAAAAATCTGCAAAA
AGCCAGATTCTACTGCAACTGAATGAGCAATTGCCAGACTAGCAGTACGCCTGCTTCTGTAGAAAAAAATAGAAGTGCTA
AAAGCTGCTGTCCAGGCATTTAAAGATGCCTGACAAAATGTTACTGAACTAGATTCACAGAAGAATGCTTCAGAGGAAAA
TCATTTTGAGGATACTTTGTGTTCAAATGATAATGCAAGTAAGTTACAGCAGGAAGAAGTTAGTATTATCAATGAGCAAA
ATGTAAAAGAAGCCAAAATTTTGGCAAAGAAACCAATAAATAACTCAAAGACAAAAATGGCCAAGATGGAACATGGACCC
AAAGCAGTAGGCATTCCAACTCCTCCATCAAAACCTTCGGGAAAGGGTTCTGTAGTTCTCCCCGAACCCCAGAAGACACC
TGCTTCCCCCAAGATGAAAACACAAAGTCAAACCAAAGAAAAAAAAGGATCTGATAGCTCACTTGGTGGTAACAGTGATG
ATGAAGAATTACATGAAGAGGAGAAGGAGTATTTTGATGACAGCATGGAAGAGAGGTTTTATAGATAGTCTTCCATGTCT
GAGGATAGTGACAGTAGTGATGACTTCTTCATTGGGAAAGTCAGACCAACACGAAAGAAAGAAAGTAGTCATCGTTCTTC
AGATAAGGAACAAAAGTCCCTCCAAAAAGAGTTACCCAAAGAAGGCACAAGTGAAACTCATTGGGACATAAATGACAAAA
ACAAGCCAAGTGCAGAACCCAGGAGATTAGAATCAGTGTTTTTCCACTCTTTATCTGGAGCTAAAGGCTCCAGAAGAGAT
TACAAAGAACAGGCTCCAAAAAGCAAAACCCTCAATTTTCCACAAAATGAAACCCAGGTCAAGAATCAGCTTAATAAAAA
TGCACAAGGAGGACTTAAAAATACAAAACAGCAATTGCAGCAGCCTCTTCATCCTTCATGGGAAGAAAGCAGAAGGCAAA
AAGAACAGCAATCTAAAATTGCTGTGTTTCAGGGGAAAAAAATCACATTTGAAGAT

Alignment

ORF - retro_ogar_1270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.41 %
• Parental protein coverage: 98.13 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LNQVVKMRKEVKRIRVLVIRKLVRSVSRLKSKKGTEDALLKNQRRAQRLLEEIHAMKELKPD-LVTKSAL
          LN..V..RK.VKRIRVLV.RKLVR.V.RLKSKKGTEDALL.NQRRAQRLLEEIHAMKELKP..LVTKSAL
Retrocopy LNNEVMKRKVVKRIRVLVFRKLVRIVNRLKSKKGTEDALLQNQRRAQRLLEEIHAMKELKPI<LVTKSAL

Parental  GEDINFEKICKKPDSTATERAVARLAVHPLLKKKIEVLKAAVQAFKEARQNVTELDSQKNASEENRSEDT
          GEDINFEKICKKPDSTATE.A.ARLAV..LL.KKIEVLKAAVQAFK.A.QNVTELDSQKNASEEN..EDT
Retrocopy GEDINFEKICKKPDSTATE*AIARLAVRLLL*KKIEVLKAAVQAFKDA*QNVTELDSQKNASEENHFEDT

Parental  LCSNDNASKLQQEEVSVINEQNGNEAKILAKKPINNSKTKMAKVEHGPKAVGLPTPPSKPSGKGSLVPPE
          LCSNDNASKLQQEEVS.INEQN..EAKILAKKPINNSKTKMAK.EHGPKAVG.PTPPSKPSGKGS.V.PE
Retrocopy LCSNDNASKLQQEEVSIINEQNVKEAKILAKKPINNSKTKMAKMEHGPKAVGIPTPPSKPSGKGSVVLPE

Parental  PQKIPASPKMKTQSQTKEKKGSDSSLGGDSDDEALHEEEKEYFDDSTEERFYRQSSMSEDSDSSDDFFIG
          PQK.PASPKM..........GSDSSLGG.SDDE.LHEEEKEYFDDS.EERFYR.SSMSEDSDSSDDFFIG
Retrocopy PQKTPASPKMXXXXXXXXXXGSDSSLGGNSDDEELHEEEKEYFDDSMEERFYR*SSMSEDSDSSDDFFIG

Parental  KVRRTRKKESSHRSSDKEQKSLQKGLPKEGTSETHWDIRNDKNKPSAEPRRLESVFFYSLSGAKGSKRDY
          KVR.TRKKESSHRSSDKEQKSLQK.LPKEGTSETHWDI.NDKNKPSAEPRRLESVFF.SLSGAKGS.RDY
Retrocopy KVRPTRKKESSHRSSDKEQKSLQKELPKEGTSETHWDI-NDKNKPSAEPRRLESVFFHSLSGAKGSRRDY

Parental  REQAPKSKTLDFPQNETQVKNQLNKNAQRGLKNTKEQLQQPLHPSWEASRRRKEQQSKIAVFQGKKITFE
          .EQAPKSKTL.FPQNETQVKNQLNKNAQ.GLKNTK.QLQQPLHPSWE.SRR.KEQQSKIAVFQGKKITFE
Retrocopy KEQAPKSKTLNFPQNETQVKNQLNKNAQGGLKNTKQQLQQPLHPSWEESRRQKEQQSKIAVFQGKKITFE

Parental  D
          D
Retrocopy D

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1270 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017177	1 retrocopy	retro_cjac_1132,
Monodelphis domestica	ENSMODG00000013487	2 retrocopies	retro_mdom_1304, retro_mdom_1705,
Otolemur garnettii	ENSOGAG00000032423	1 retrocopy	retro_ogar_1270 ,
Tarsius syrichta	ENSTSYG00000006869	1 retrocopy	retro_tsyr_1456,