RetrogeneDB ID: retro_ogar_2991

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873693.1:3588161..3589586(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA5
• Ensembl ID: ENSOGAG00000011924
• Aliases: None
• Description: karyopherin alpha 5 (importin alpha 6) [Source:HGNC Symbol;Acc:6398]

Sequence

>retro_ogar_2991
GATACCATGGCTAGTCCAGGGAAGGATAACTATAGAATGAAAAGTTATAAGAATAAAGCCCTGAATCCTCAAGAGATGCG
TAGACACAGAGAAAAAGAAGGAATACAGCTTGGAAAACAAAAAAGGGAAGAACAGTTGTTGAAACACAGAAATGTCTCTT
TACCCAGAAATAATGAGTCTATGCTAGAATGTCCTATACAGAATCCGGATATCAGTTCCACTGTACCCACTCCAGAGGAA
GAAGTCATTACTACAGATACGGTTCAGATGATTTTTTCTAATAATGCTGATCAATGGCTAACAGCAACACAGAAATTTAG
AAAGCTGCTTTCTAAAGAATCTAATCCGCCAATTGATCAAGTTATACAGAAACCAGGAGTCATACAGAGATTTGTGAAAT
TTCTTGAAAGAAATGAAAACTGTACTCCACAATTTGAAGCTGCATGGGCATTGACTAAGATAGCATCCAGAACTTTTCTG
CATACCAAGGTAGTGATTGAAACTGGGGCTGTTCCAATTTTTGTCAAACTTAATTCTGAATATGAAGATCTTCAAGAACA
GGCGGTTTGGGCACTTGGTAATATTGCAGATGACGACAATGCAGAATGCAGAGATTTTGTATTGAATTGTGAAATACTTC
CACCTCATTAAGAGTTCTTAAAAAATTCTAATAGACTTACAACAAGAAGAAATGCTGTGTGGACCCTCTCAAATTTATGT
AGAGGCAACAACCCTCCTCCAAACTTTAGTAAGGTTTCACCTTGTTTAAATGTTCTGTCACGATTATTGTTTAGCAGTGA
CTCAGATGTGTTAGCAGATGTGTGTTGGGCCCTCTCTTATCTCTCCAATAGACCCAATTATCAAATTCAAGCAGTCATTG
ATTCTGGAGTATGTTGAAGATTGGTGAAACTTTTGATACACAATGATTATAAAGTTGCATCACCTGCCTTACGGGCAGTT
GGTAATATTGTGGCTGGTGATGATATTCAGACACAGGTAATTTTGAATGGTTCTGCATTACCCCGTCTCTTACATTTATT
GAGTAGCCCAAAAGAGTGAATTAGAAAAGAAGCTTGCTGGACAGTTTCTAACATCACTGCTGGAAATAGAGCTCAGATTC
AGGCAGTTATAGATGCAAATATTTTTCCTGTTTTGATTGAGATTCTTCAGAAAGCAGAGTTTCCCACCAGAAAAGCAGCA
GGTTGGGTTATAACTAATGCAACGTCAGGAGGCACTCCGGAGCAGATAAAGTATTTGGTAGCTTTAGGCTACATTAAATC
ACTTTGTGACCTTTTGATTGTTATGGACTCTAAAATAGTCCAAGTGGCTTTAAATGGACTTGAAAATATTTTACATCTTG
GAGAACAAGAATCTGAGCAGAATGGAATAGGCATTAATCCATACTGTGCTCTCATTGAAGAAGCA

Alignment

ORF - retro_ogar_2991 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.87 %
• Parental protein coverage: 88.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DAMASPGKDNYRMKSYKNKALNPQEMRRRREEEGIQLRKQKREEQLFKRRNVSLPRNDESMLESPIQDPD
          D.MASPGKDNYRMKSYKNKALNPQEMRR.RE.EGIQL.KQKREEQL.K.RNVSLPRN.ESMLE.PIQ.PD
Retrocopy DTMASPGKDNYRMKSYKNKALNPQEMRRHREKEGIQLGKQKREEQLLKHRNVSLPRNNESMLECPIQNPD

Parental  ISSTVPIPEEEVITTDMVQMIFSNNVDQQLTATQKFRKLLSKEPNPPIDQVIQKPGVVQRFVKFLERNEN
          ISSTVP.PEEEVITTD.VQMIFSNN.DQ.LTATQKFRKLLSKE.NPPIDQVIQKPGV.QRFVKFLERNEN
Retrocopy ISSTVPTPEEEVITTDTVQMIFSNNADQWLTATQKFRKLLSKESNPPIDQVIQKPGVIQRFVKFLERNEN

Parental  CTLQFEAAWALTNIASGTFLHTKVVIETGAVPIFIKLLNSEHEDVQEQAVWALGNIA-GDNAECRDFVLN
          CT.QFEAAWALT.IAS.TFLHTKVVIETGAVPIF.K.LNSE.ED.QEQAVWALGNIA..DNAECRDFVLN
Retrocopy CTPQFEAAWALTKIASRTFLHTKVVIETGAVPIFVK-LNSEYEDLQEQAVWALGNIADDDNAECRDFVLN

Parental  CEILPPLLELLKNSNRLTTTRNAVWALSNLCRGKNPPPNFSKVSPCLNVLSRLLFSSDPDVLADVCWALS
          CEILPP..E.LKNSNRLTT.RNAVW.LSNLCRG.NPPPNFSKVSPCLNVLSRLLFSSD.DVLADVCWALS
Retrocopy CEILPPH*EFLKNSNRLTTRRNAVWTLSNLCRGNNPPPNFSKVSPCLNVLSRLLFSSDSDVLADVCWALS

Parental  YLSDGPNDKIQAVIDSGVCRRLVELLMHNDYKVVSPALRAVGNIVTGDDIQTQVILNCSALPCLLHLLSS
          YLS..PN..IQAVIDSGVC.RLV.LL.HNDYKV.SPALRAVGNIV.GDDIQTQVILN.SALP.LLHLLSS
Retrocopy YLSNRPNYQIQAVIDSGVC*RLVKLLIHNDYKVASPALRAVGNIVAGDDIQTQVILNGSALPRLLHLLSS

Parental  PKESIRKEACWTVSNITAGNRAQIQAVIDANIFPVLIEILQKAEFRTRKEAAWAITNATSGGTPEQIRYL
          PKE.IRKEACWTVSNITAGNRAQIQAVIDANIFPVLIEILQKAEF.TRK.A.W.ITNATSGGTPEQI.YL
Retrocopy PKE*IRKEACWTVSNITAGNRAQIQAVIDANIFPVLIEILQKAEFPTRKAAGWVITNATSGGTPEQIKYL

Parental  VALGCIKPLCDLLTVMDSKIVQVALNGLENILRLGEQESKQNGIGINPYCALIEEA
          VALG.IK.LCDLL.VMDSKIVQVALNGLENIL.LGEQES.QNGIGINPYCALIEEA
Retrocopy VALGYIKSLCDLLIVMDSKIVQVALNGLENILHLGEQESEQNGIGINPYCALIEEA

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_2991 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000017826	1 retrocopy	retro_mdom_554,
Otolemur garnettii	ENSOGAG00000011924	1 retrocopy	retro_ogar_2991 ,
Otolemur garnettii	ENSOGAG00000027672	7 retrocopies	retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Otolemur garnettii	ENSOGAG00000031106	3 retrocopies	retro_ogar_1289, retro_ogar_3237, retro_ogar_353,