RetrogeneDB ID: retro_ogar_2604

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873638.1:1948491..1949932(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000027842
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RSL1D1
• Ensembl ID: ENSOGAG00000015151
• Aliases: None
• Description: ribosomal L1 domain containing 1 [Source:HGNC Symbol;Acc:24534]

Sequence

>retro_ogar_2604
ATGGAGGGCTCAGCTTCCATGCGGTTGCCAAGCACAGAGGCGACTGCAGCTTCCACCTCAATTCCAGAGGCTCCGAGCGT
AGAGAAACAGCTGGATAAAAATCAAATTCGAAAGGCAGTGGAAGCTCTCTTGGCACATTGCAAGACCAGGAAAAACGATA
ATGGATTCCTTTTGAATGAGAATGAAAATTTATTTTTAATGGTGAAATTGTGGAAAATTCCAAGTAAAGAACCGAGGGTC
AGATTGCCCTTGCCTCATGGTATTCGATCAGATTTAGAAGAAATCTGTTTATTTACCAAGGATGAACCCAATAAAACTCC
TGAACAGACAGAAGTTTCTATAGAAAGCTTTTGAACAAGCATGGCATTAAAACCATATCTCGGATTATACCACTCCAAAC
TTTAAAAAAGGAATATAAACCCTATGAAGCCAAGCTCAGCCTTATGAGTAGTTTTGACTTTTTCCTTACTGATGCCAGAA
TTGGGCAGCTTTTACCCACACACACTGGGAGACATTTCTATCAAAGAAAGAAAGTTCCAGTAGCTGTGAATCTTCTAACC
AAGAATTTATCAACAGAGATCAATGAATCTATAGGTGGAACAGTCTTAAACATCTCTAAAAGTGGTTCTTGCAGCACTAT
ACGCATTGGTCACACTGCAGTGCAGATTGAGCATATCATTGAAAACATTATTACTGTCACAAAAGGGCTTTCAGAAAAAT
TGCCAGAGAAGTGGAAGAGTGTGAAACTCATGTTTGTGAAAACTGAGAGATCGGTTGCCCTCCCCATCTTCTCTTCATTT
GTCACCAGTTGGGATGAAAATACCAAACGTTATCTTCCTAAGAAAAAAGTGACAAAGAAAAATCCGCGACGACGTCTTGA
AAAACTAAAGTGGAAGAAGAAGAGGCAGCAGGCTTCATCAGTCTTAACAAAAAATGATGCAGCACCTAAAAGTGGTGCTC
TGGTGAAGAAACCCGGACCCCAGAAGGAAAAGGGCCCGGGACATGGGAAGAAAAAACGTGGCAAACGTGGCAGAGTCAAA
GCCCAACTTAAAGTGACAAACGGCTCTGAAGATGAAGTTCCACAGCTGGTACCAATAGGAACAGCTCCAGCTAAAGAAAA
TGTAGAGACTCAAAAACATACCGTAGGAAAGAAGTCTTCAAAAAAGAGTCCTGGTCCCACTACACCTCATGGGAAGAAGA
GAAAGGCCTTACCAGCTTCAGACACCGTGAAAGCTGCAGAGCCTGAGACTCCAGGTAAAGCTCCAGGAAAGAAGCCAAAA
ATCAGAGAAGAGGCAGAGAAGGAAAGAAATCTTTTACTGACCAAAAAAGACCCAAGACAGACTCCAAAAAGCCAGAGGCC
AAGATCTTTGCTACTTCTACCAAACCTGCAAGAAAAGCTCCCCACACCCCTAAACGATTGCCCAAAGTCCCTCATTCGAC
C

Alignment

ORF - retro_ogar_2604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEGSASMPPPSTEATAPSTSIPEAPSAEEQLDKNQIRKAVEALLAHCKSRKNDNGFLLNENENLFLMVIL
          MEGSASM..PSTEATA.STSIPEAPS.E.QLDKNQIRKAVEALLAHCK.RKNDNGFLLNENENLFLMV.L
Retrocopy MEGSASMRLPSTEATAASTSIPEAPSVEKQLDKNQIRKAVEALLAHCKTRKNDNGFLLNENENLFLMVKL

Parental  WKIPSKELRVRLPLPHGIRSDLEEICLFTKDEPNKTPEQTE-RFYRKLLNKHGIKTISRIIPLQTLKKEY
          WKIPSKE.RVRLPLPHGIRSDLEEICLFTKDEPNKTPEQTE..FYRKLLNKHGIKTISRIIPLQTLKKEY
Retrocopy WKIPSKEPRVRLPLPHGIRSDLEEICLFTKDEPNKTPEQTE<SFYRKLLNKHGIKTISRIIPLQTLKKEY

Parental  KPYEAKLRLMSSFDFFLTDARIRRLLPTHIGRHFYQRKKVPVSVNLLTKNLSTEINESIGGTVLNISKSG
          KPYEAKL.LMSSFDFFLTDARI..LLPTH.GRHFYQRKKVPV.VNLLTKNLSTEINESIGGTVLNISKSG
Retrocopy KPYEAKLSLMSSFDFFLTDARIGQLLPTHTGRHFYQRKKVPVAVNLLTKNLSTEINESIGGTVLNISKSG

Parental  SCSTIRIGHTAMQIEHITENIIAVAKGLSEKLPEKWKSVKLMFVKTERSVALPIFSSFVTSWDENTKRYL
          SCSTIRIGHTA.QIEHI.ENII.V.KGLSEKLPEKWKSVKLMFVKTERSVALPIFSSFVTSWDENTKRYL
Retrocopy SCSTIRIGHTAVQIEHIIENIITVTKGLSEKLPEKWKSVKLMFVKTERSVALPIFSSFVTSWDENTKRYL

Parental  PKKKDNSVTKKNPRRRLEKLKW-KKRQQASSVSTKDNAAPKSGALVKKPGPQKEKGPGHGKKKRSKRGRV
          PKKK...VTKKNPRRRLEKLKW.KKRQQASSV.TK..AAPKSGALVKKPGPQKEKGPGHGKKKR.KRGRV
Retrocopy PKKK---VTKKNPRRRLEKLKWKKKRQQASSVLTKNDAAPKSGALVKKPGPQKEKGPGHGKKKRGKRGRV

Parental  KAQLKVTNDSEDEIPQLVPIGRTAPAKENVETQKHTIGKKSSKKSPGPTTPHGKKRKALPASDAVKAAEP
          KAQLKVTN.SEDE.PQLVPIG.TAPAKENVETQKHT.GKKSSKKSPGPTTPHGKKRKALPASD.VKAAEP
Retrocopy KAQLKVTNGSEDEVPQLVPIG-TAPAKENVETQKHTVGKKSSKKSPGPTTPHGKKRKALPASDTVKAAEP

Parental  ETPGKAPGKKPKIREEAEKEGNLLLTKKDPRQTP-KKPEAKVFATSTKPARKAPHTPKRLPKVPHST
          ETPGKAPGKKPKIREEAEKE.NLLLTKKDPRQTP.KKPEAK.FATSTKPARKAPHTPKRLPKVPHST
Retrocopy ETPGKAPGKKPKIREEAEKERNLLLTKKDPRQTP<KKPEAKIFATSTKPARKAPHTPKRLPKVPHST

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_2604 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018865	2 retrocopies	retro_cfam_1937, retro_cfam_691,
Choloepus hoffmanni	ENSCHOG00000010827	2 retrocopies	retro_chof_1617, retro_chof_852,
Callithrix jacchus	ENSCJAG00000008375	1 retrocopy	retro_cjac_2154,
Cavia porcellus	ENSCPOG00000010630	3 retrocopies	retro_cpor_1262, retro_cpor_276, retro_cpor_822,
Loxodonta africana	ENSLAFG00000013664	1 retrocopy	retro_lafr_364,
Myotis lucifugus	ENSMLUG00000000784	1 retrocopy	retro_mluc_1309,
Monodelphis domestica	ENSMODG00000029494	2 retrocopies	retro_mdom_1240, retro_mdom_573,
Otolemur garnettii	ENSOGAG00000015151	1 retrocopy	retro_ogar_2604 ,
Rattus norvegicus	ENSRNOG00000048608	1 retrocopy	retro_rnor_2771,
Sarcophilus harrisii	ENSSHAG00000016705	1 retrocopy	retro_shar_836,