RetrogeneDB ID: retro_pabe_88

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:38573147..38575172(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000008261
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KIF2C
• Ensembl ID: ENSPPYG00000001427
• Aliases: None
• Description: kinesin family member 2C [Source:HGNC Symbol;Acc:6393]

Sequence

>retro_pabe_88
ATGGCCAGCCAGTTCTGCCTTCCTGAATCCCCATGCCTCTCGCCCCTGAAACCCTTGAAGCCACATTTCGGAGACATCCA
AGTGGGCATCTACGTGGCGATCCAGCGCAGTGACAAGCGGATCCACCTCGCTGTGGTAACGGAGATCAACAGAGAAAACT
ATTGGGTCACGGTAGAGTGGGTGGAGAAAGCAGTCAAAAAAGGCAAGAAGATTGACCTGGAGACCATACTCCTGCTGAAT
CCAGCTCTGGACTCTGCTGAACACCCCATGCCGCCCCCGCCCTTATCCCCCTTGGCTCCGGCGCCCTCTTCGGCCATCAG
GGACCAGCGTACCGCCACGAAATGGGTTGTGATGATCCCCCAGAAAAACAAAACAGCCTCTGGGGACAGCCTGGACGTGA
GGATCCCCAGCAAACCTTGTCTGATGAAGCAGAAAAAGTCTCCTTGCCTCTGGGAAATCCAGAAACTGCAGAAGCAGCGG
GAAAAGCGCAGGCGGCTGCAGCAGGAGATCCGAGCTAGACGTGCCCTCGATGTCAACATCAGAAACCCCAACTACGAAAT
CATGCACATGATCGAAGAGTATCGCAGGCACCTGGACAGCAGCAAGATTTCAGTCCTGGAGCCCCCGCAAGAACATCGCA
TCTGCGTCTGCGTGAGGAAGCGGCCTCTCAACCAGCGAGAGACAACCTTGAAGGACCTGGATATCATCACCGTCCCCTCG
GACAATGTGGTTATGGTGCATGAGTCCAAGCAAAAGGTGGACCTCACTCGCTACCTGCAGAACCAGACCTTCTGCTTCGA
CCATGCCTTCGACGACAAAGCCTCCAACGAGTTGGTGTACCAGTTCACCGCCCAGCCACTGGTGGAGTCCATCTTCCGCA
AGGGCATGGCCACCTGCTTTGCCTATGGGCAGACGGGAAGTGGGAAGACGTACACCATGGGTGGAGACTTTTCAGGAAGG
GCCCAAGATTGTTCTAAGGGCATTTATGCTCTGGTGGCACAGGATGTCTTTCTCCTGCTCAGAAACTCCACATATGAGAA
GCTGGACCTCAAAGTCTATGGGACATTTTTTGAGATTTATGGGGGCAAGGTGTATGATTTGTTGAACTGGAAGAAGAAAC
TGCAAGTCCTTGAGGATGGCAATCAGCAAATCCAAGTGGTCGGGCTGCAGGAGAAAGAGGTGTGTTGTGTGGAGGAAGTG
CTGAACCTGGTGGAAATAGGGAATAGCTGTCGGACTTCCAGGCAAACATCTGTCAACGCTCACTCATCCAGGAGCCATGC
AGTGTTCCAGATCATCTTGAAGTCAGGAGGGATATTGCATGGCAAGTTTTCCCTCGTTGATTTAGCTGGGAATGAAAGGG
GAGCAGATACGACCAAGGCCAGCCGGAAAAGGCAGCTGGAAGGGGCAGAGATTAACAAGAGTCTTCTAGCCCTCAAAGAA
TGTATTCTAGCTTTGGGTCAGAACAAGCCTCACACCCCATTCAGAGCCAGCAAACTCACACAGGTGCTCCGGGACTCCTT
TATAGGCCAGAACTCCTCCACTTGCATGATCGCTACTATCTCTCCAGGAATGACCTCTTGTGAAAACACTCTCAACACTT
TAAGATATGCAAACAGAGTAAAAAAATTAAATGTAGATGTAAGGCCATACCATCGTGGCCTCTATCCGATTGGACATGAG
ACACCAAGGATGTTAAAAAGTCACATCGGAAATTCAGAAATGTCCCTTCAGAGGGATGAATTTATTAAAATACCTTATGT
ACAGTGTGAGGGGCAGCACAAAGAGATTGAAGAGGTTGAAACATTACCCATTCCGTTAGGGAAGGATACCACAACTTCAG
GGAAGGGATCTAGCCAATGGTTGGAAAATATCCAGGAGAGAGCTGGTGGAGTAAACCATGATATTGATTTTTGCGTTGCC
CGGTCTTTGTCCATTTTGGAGCAGAAAATTGATGTTCTGACCGAGATCCAAAAGAAACTGAAATTATTACGAGCTGACCT
CCACATGAAGAGCAAGGTAGAGTGA

Alignment

ORF - retro_pabe_88 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.76 %
• Parental protein coverage: 57.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANPVNSVRRKSCLVKEVEKMKNKREEKKAQNSEMRMKRAQEYDSSFPNWEFARMIKEFRATLECHPLTMT
          ..P......KS....E..K....RE.......E.R..RA.......PN.E...MI.E.R..L........
Retrocopy SKPCLMKQKKSPCLWEIQKLQKQREKRRRLQQEIRARRALDVNIRNPNYEIMHMIEEYRRHLDSSKISVL

Parental  DPIEEHRICVCVRKRPLNKQELAKKEIDVISIPSKCLLLVHEPKLKVDLTKYLENQAFCFDFAFDETASN
          .P..EHRICVCVRKRPLN..E...K..D.I..PS.....VHE.K.KVDLT.YL.NQ.FCFD.AFD..ASN
Retrocopy EPPQEHRICVCVRKRPLNQRETTLKDLDIITVPSDNVVMVHESKQKVDLTRYLQNQTFCFDHAFDDKASN

Parental  EVVYRFTARPLVQAIFEGGKATCFAYGQTGSGKTHTMGGDLSGKAQNASKGIYAMASRDVFLLKNQPCYR
          E.VY.FTA.PLV..IF..G.ATCFAYGQTGSGKT.TMGGD.SG.AQ..SKGIYA....DVFLL.....Y.
Retrocopy ELVYQFTAQPLVESIFRKGMATCFAYGQTGSGKTYTMGGDFSGRAQDCSKGIYALVAQDVFLLLRNSTYE

Parental  KLGLEVYVTFFEIYNGKLFDLLNKKAKLRVLEDGKQQVQVVGLQEHLVNSADDVIKMIDMGSACRTSGQT
          KL.L.VY.TFFEIY.GK..DLLN.K.KL.VLEDG.QQ.QVVGLQE..V.....V......G..CRTS.QT
Retrocopy KLDLKVYGTFFEIYGGKVYDLLNWKKKLQVLEDGNQQIQVVGLQEKEVCCVEEVLNLVEIGNSCRTSRQT

Parental  FANSNSSRSHACFQILLRAKGRMHGKFSLVDLAGNERGADTSSADRQTRMEGAEINKSLLALKECIRALG
          ..N..SSRSHA.FQI.L...G..HGKFSLVDLAGNERGADT..A.R....EGAEINKSLLALKECI.ALG
Retrocopy SVNAHSSRSHAVFQIILKSGGILHGKFSLVDLAGNERGADTTKASRKRQLEGAEINKSLLALKECILALG

Parental  QNKSHTPFRESKLTQVLRDSFIGENSRTCMIATISPGISSCEYTLNTLRYADRVKELS
          QNK.HTPFR.SKLTQVLRDSFIG.NS.TCMIATISPG..SCE.TLNTLRYA.RVK.L.
Retrocopy QNKPHTPFRASKLTQVLRDSFIGQNSSTCMIATISPGMTSCENTLNTLRYANRVKKLN

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.61 RPM
SRP007412_cerebellum	0.00 RPM	1.70 RPM
SRP007412_heart	0.00 RPM	0.24 RPM
SRP007412_kidney	0.00 RPM	0.80 RPM
SRP007412_liver	0.00 RPM	1.25 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_88 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_88 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_88 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_69
Equus caballus	retro_ecab_32

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000028678	1 retrocopy	retro_mmus_1251,
Otolemur garnettii	ENSOGAG00000006916	1 retrocopy	retro_ogar_1892,
Pongo abelii	ENSPPYG00000001427	1 retrocopy	retro_pabe_88 ,
Pteropus vampyrus	ENSPVAG00000009856	1 retrocopy	retro_pvam_3,
Sus scrofa	ENSSSCG00000003931	1 retrocopy	retro_sscr_25,
Tursiops truncatus	ENSTTRG00000000748	1 retrocopy	retro_ttru_1318,
Drosophila melanogaster	FBgn0030268	2 retrocopies	retro_dmel_1, retro_dmel_2,