RetrogeneDB ID: retro_ptro_102

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:95416350..95417940(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000033789
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KPNA7
• Ensembl ID: ENSPTRG00000019446
• Aliases: None
• Description: karyopherin alpha 7 (importin alpha 8) [Source:HGNC Symbol;Acc:21839]

Sequence

>retro_ptro_102
ATGTCCACCAACGAGAATGCTAATACACCAGCTGCCCGTCTTCACAGATTCAAGAACAAGGGAAAAGACAGTACAGAAAT
GAGGCGTCGCAGAATAGAGGTCAATGTGGAGCTGAGGAAAGCTAAGAAGGATGACCAGATGCTGAAGAGGAGAAATGTAA
GCTCATTTCCTGATGATGCTACTTCTCCGCTGCAGGAAAACCGCAACAACCAGGGCACTGTAAATTGGTCTGTTGATGAC
ATTGTCAAAGGCATAAATAGCAGCAATGTGGAAAATCAGCTCCAAGCTACTCAAGCTGCCAGGAAACTACTTTCCAGAGA
AAAACAGCCCCCCATAGACAACATAATCCGGGCTGGTTTGATTCCGAAATTTGTGTCCTTCTTGGGCAGAACTGATTGTA
GTCCCATTCAGTTTGAATCTGCTTGGGCACTCACTAACATTGCTTCTGGGACATCAGAACAAACCAAGGCTGTGGTAGAT
GGAGGTGCCATCCCAGCATTCATTTCTCTGTTGGCATCTCCCCATGCTCACATCAGTGAACAAGCTGTCTGGGCTCTAGG
AAACATTGCAGGTGATGGCTCAGTGTTCCGAGACTTGGTTATTAAGTACGGTGCAGTTGACCCACTGTTGGCTCTCCTTG
CAGTTCCTGATATGTCATCTTTAGCATGTGGCTACTTACGTAATCTTACCTGGACACTTTCTAATCTTTGCCGCAACAAG
AATCCTGCACCCCCGAGAGATGCTGTTGAGCAGATTCTTCCTACCTTAGTTCGGCTCCTGCATCATGATGATCCAGAAGT
ATTAGCAGATACCTGCTGGGCTATTTCCTACCTTACTGATGGTCCAAATGAACGAATTGGCATGGTCGTGAAAACAGGAG
TTGTGCCCCAACTTGTGAAGCTTCTAGGAGCTTCTGAATTGCCAATTGTGACTCCTGCCCTAAGAGCCATAGGGAATATT
GTCACTGGTACAGATGAACAGACTCAGGTTGTGATTGATGCAGGAGCACTCGCCGTCTTTCCCAGCCTGCTCACCAACCC
CAAAACTAACATTCAGAAGGAAGCTACGTGGACAATGTCAAACATCACAGCCGGCCGCCAGGACCAGATACAGCAAGTTG
TGAATCATGGATTAGTCCCATTCCTTGTCAGTGTTCTCTCTAAGGCAGATTTTAAGACACAAAAGGAAGCTGTGTGGGCC
GTGACCAACTATACCAGTGGTGGAACAGTTGAACAGATTGTGTACCTTGTTCACTGTGGCATAATAGAACCGTTGATGAA
CCTGTTATCTGCAAAAGATACCAAGATTATTCTGGTTATCCTGGATGCCATTTCAAATATCTTTCAGGCTGCTGAGAAAC
TAGGTGAAATTGAGAAACTTAGTATAATGATTGAAGAATGTGGAGGCTTAGACAAAATTGAAGCTCTACAAAACCATGAA
AATGAGTCTGTGTATAAGGCTTCGTTAAGCTTAATTGAGAAGTATTTCTCTGTAGAGGAAGAGGAAGATCAAAACGTTGT
ACCAGAAACTACCTCTGAAGGCTACACTTTCCAAGTTCAGGATGGGGCTCCTGGGACCTTTAACTTTTAG

Alignment

ORF - retro_ptro_102 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.71 %
• Parental protein coverage: 97.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DAPEERRRKFKYRGKDASLRRQQRMAVSLELRKAKKDEQTLKRRNIMSFCPDTPS---EKTAKGVAVSLT
          ..P..R...FK..GKD....R..R..V..ELRKAKKD.Q.LKRRN..SF..D..S...E.......V...
Retrocopy NTPAARLHRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQENRNNQGTVNWS

Parental  LGEIIEGVNSSDPVLCFQATQTARKMLSREKNPPLKLVIEAGLIPRMVEFLKSSLYPCLQFEAAWALTNI
          ...I..G.NSS......QATQ.ARK.LSREK.PP....I.AGLIP..V.FL........QFE.AWALTNI
Retrocopy VDDIVKGINSSNVENQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGRTDCSPIQFESAWALTNI

Parental  ASGTSEQTRAVVEGGAIQPLIELLSSSNVAVCEQAVWALGNIAGDGPEFRDNVITSNAIPHLLALIS---
          ASGTSEQT.AVV.GGAI...I.LL.S......EQAVWALGNIAGDG..FRD.VI...A...LLAL.....
Retrocopy ASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPLLALLAVPD

Parental  -PTLPITFLRNITWTLSNLCRNKNPYPCDTAVKQILPALLHLLQHQDSEVLSDACWALSYLTDGSNKRIG
          ...L....LRN.TWTLSNLCRNKNP.P...AV.QILP.L..LL.H.D.EVL.D.CWA.SYLTDG.N.RIG
Retrocopy MSSLACGYLRNLTWTLSNLCRNKNPAPPRDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTDGPNERIG

Parental  QVVNTGVLPRLVVLMTSSELNVLTPSLRTVGNIVTGTDEQTQMAIDAGMLNVLPQLLQHNKPSIQKEAAW
          .VV.TGV.P.LV.L...SEL...TP.LR..GNIVTGTDEQTQ..IDAG.L.V.P.LL...K..IQKEA.W
Retrocopy MVVKTGVVPQLVKLLGASELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSLLTNPKTNIQKEATW

Parental  ALSNVAAGPCHHIQQLLAYDVLPPLVALLKNGEFKVQKEAVWTVANFATGATMDQLIQLVHSGVLEPLVN
          ..SN..AG....IQQ.......P.LV..L....FK.QKEAVW.V.N...G.T..Q...LVH.G..EPL.N
Retrocopy TMSNITAGRQDQIQQVVNHGLVPFLVSVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCGIIEPLMN

Parental  LLTAPDVKIVLIILDVISCILQAAEKRSEKENLCLLIEELGGIDRIEALQLHENRLIGQSALNIIEKHFG
          LL.A.D.KI.L.ILD.IS.I.QAAEK..E.E.L...IEE.GG.D.IEALQ.HEN.......L..IEK.F.
Retrocopy LLSAKDTKIILVILDAISNIFQAAEKLGEIEKLSIMIEECGGLDKIEALQNHENESVYKASLSLIEKYFS

Parental  EEEDESQTLLSQVIDQDYEF
          .EE.E.Q..........Y.F
Retrocopy VEEEEDQNVVPETTSEGYTF

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	2.43 RPM	0.05 RPM
SRP007412_cerebellum	2.72 RPM	0.14 RPM
SRP007412_heart	1.22 RPM	0.00 RPM
SRP007412_kidney	1.52 RPM	0.05 RPM
SRP007412_liver	1.60 RPM	0.07 RPM
SRP007412_testis	92.53 RPM	4.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_102 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_102 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015125	2 retrocopies	retro_cfam_459, retro_cfam_861,
Choloepus hoffmanni	ENSCHOG00000004243	1 retrocopy	retro_chof_805,
Callithrix jacchus	ENSCJAG00000015943	1 retrocopy	retro_cjac_2964,
Equus caballus	ENSECAG00000000554	1 retrocopy	retro_ecab_981,
Echinops telfairi	ENSETEG00000000096	1 retrocopy	retro_etel_1548,
Homo sapiens	ENSG00000185467	1 retrocopy	retro_hsap_3337,
Mus musculus	ENSMUSG00000038770	2 retrocopies	retro_mmus_2844, retro_mmus_3301,
Nomascus leucogenys	ENSNLEG00000010827	1 retrocopy	retro_nleu_1680,
Otolemur garnettii	ENSOGAG00000031106	3 retrocopies	retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps	ENSOPRG00000015434	2 retrocopies	retro_opri_1101, retro_opri_118,
Pongo abelii	ENSPPYG00000017369	1 retrocopy	retro_pabe_2750,
Pan troglodytes	ENSPTRG00000019446	2 retrocopies	retro_ptro_102 , retro_ptro_2142,
Tupaia belangeri	ENSTBEG00000009007	3 retrocopies	retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus	ENSTTRG00000002998	2 retrocopies	retro_ttru_1426, retro_ttru_430,