RetrogeneDB ID: retro_pabe_1558

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:44571806..44572766(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WBP11
• Ensembl ID: ENSPPYG00000004323
• Aliases: None
• Description: WW domain binding protein 11 [Source:HGNC Symbol;Acc:16461]

Sequence

>retro_pabe_1558
AAATAGCTGCGTGAAACCTTTGAACATATTCTACGACTCTATGAAAAAGAGAATCCAGATATTTAGAAAGAATTGAGAAA
GCTAGAAATAGAATATGAACAGAAGAGGGCTCAACTTAACCAATATTTGAATGCTGTTGAGAATGCCCAGCACATGGAAG
TGGAGAGTATTCCTTTACCAGATATGCCACATGCTCCTTCAAACATTTTGATCCAGGACATTCCACTTCCTGGTGCCTAG
CCACCCTCCATCCTTAAGAAACCCTCAGCCTATGGACCTCCAACTCAGGCAGTTTCTATCCTTCTCTTCTTGGGACGTGG
TGTTCCACATTTGCCCCCTGGCAGAAAACTTCTTGGCCCTCCCCCTGGTCCACCCCCTCCTCAAGTCATGCAGATGTATG
GCCGTAAAGTGGGTGTTGCCCTAGATCTTCCCCCTTGTAGGTGAGAGGAAGACATGGTACATAGTCCTGAAATTGCCCAG
CGAGGTCATGATGATGATGTTTTTAGCACCAGTGAAGATGATGGCTATCCTGAGGACATGGATCAAGATAAGCATGATGA
CAGTACTGATGACAGTGACACCGACGGGTCAGATTGAGAAAGTGTGCACCGTGATGATGGTGGGAGAGACAACAATGAAA
AAAAGAAGTCAGGTCTGAGTGTACGGTTTGCAGATATGCCTGGAAAATCAAGGAAGAAAAAAAAGAACATGAAGGAACTG
ACTCCTCTTGAAGCCACGATGCTTCATATGGCAGGTCAAGAAATCCCTGAGGAGGGACGGGAAGTAGAGGAATTTTCAGA
GGACGATGATGAAGATGATTCTGATGACTCTAAAGCAGAAAAACAATCACAAAAATACCATAAAGAGGAATGGCATTCTG
ATGGCACATCCACTGCGTCTTCACAGCAGCAGGCTCCTCCGCAGTCTGTTCCTCCTTCTCAGATACAAGCACCTCCCATG

Alignment

ORF - retro_pabe_1558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.15 %
• Parental protein coverage: 50.7 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKLRETFERILRLYEKENPDIYKELRKLEVEYEQKRAQLSQYFDAVKNAQHVEVESIPLPDMPHAPSNIL
          K.LRETFE.ILRLYEKENPDI.KELRKLE.EYEQKRAQL.QY..AV.NAQH.EVESIPLPDMPHAPSNIL
Retrocopy K*LRETFEHILRLYEKENPDI*KELRKLEIEYEQKRAQLNQYLNAVENAQHMEVESIPLPDMPHAPSNIL

Parental  IQDIPLPGAQPPSILKKTSAYGPPTRAVSILPLLGHGVPRLPPGRKPPGPPPGPPPPQVVQMYGRKVGFA
          IQDIPLPGA.PPSILKK.SAYGPPT.AVSIL..LG.GVP.LPPGRK..GPPPGPPPPQV.QMYGRKVG.A
Retrocopy IQDIPLPGA*PPSILKKPSAYGPPTQAVSILLFLGRGVPHLPPGRKLLGPPPGPPPPQVMQMYGRKVGVA

Parental  LDLPPRRRDEDMLYSPELAQRGHDDDVSSTSEDDGYPEDMDQDKHDDSTDDSDTDKSDGESDGDEFVHRD
          LDLPP.R..EDM..SPE.AQRGHDDDV.STSEDDGYP.....D...D..DDS.TD.SD......E.VHRD
Retrocopy LDLPPCR*EEDMVHSPEIAQRGHDDDVFSTSEDDGYP----EDMDQDKHDDS-TDDSDTDGSD*ESVHRD

Parental  DGERDNNEEKKSGLSVRFADMPGKSRKKKKNMKELTPLQAMMLRMAGQEIPEEGREVEEFSEDDDDDDSD
          DG.RDNNE.KKSGLSVRFADMPGKSRK...NMKELTPL.A.ML.MAGQEIPEEGREVEEFSEDDD.DDSD
Retrocopy DGGRDNNEKKKSGLSVRFADMPGKSRKXXXNMKELTPLEATMLHMAGQEIPEEGREVEEFSEDDDEDDSD

Parental  DSEAEKQSQKQHKEESHSDGTSTASSQQQAPPQSVPPSQIQAPPM
          DS.AEKQSQK.HKEE.HSDGTSTASSQQQAPPQSVPPSQIQAPPM
Retrocopy DSKAEKQSQKYHKEEWHSDGTSTASSQQQAPPQSVPPSQIQAPPM

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	72.76 RPM
SRP007412_cerebellum	0.00 RPM	38.18 RPM
SRP007412_heart	0.00 RPM	29.62 RPM
SRP007412_kidney	0.00 RPM	36.63 RPM
SRP007412_liver	0.00 RPM	22.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1558 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1558 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1878
Pan troglodytes	retro_ptro_1260
Gorilla gorilla	retro_ggor_1375
Macaca mulatta	retro_mmul_1329

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014759	1 retrocopy	retro_btau_20,
Canis familiaris	ENSCAFG00000012926	2 retrocopies	retro_cfam_1369, retro_cfam_1911,
Callithrix jacchus	ENSCJAG00000021611	1 retrocopy	retro_cjac_1737,
Homo sapiens	ENSG00000084463	2 retrocopies	retro_hsap_1878, retro_hsap_4719,
Gorilla gorilla	ENSGGOG00000004448	3 retrocopies	retro_ggor_1375, retro_ggor_1711, retro_ggor_2932,
Macropus eugenii	ENSMEUG00000013971	1 retrocopy	retro_meug_1952,
Myotis lucifugus	ENSMLUG00000015216	1 retrocopy	retro_mluc_1074,
Macaca mulatta	ENSMMUG00000019299	1 retrocopy	retro_mmul_1329,
Monodelphis domestica	ENSMODG00000017949	1 retrocopy	retro_mdom_143,
Mustela putorius furo	ENSMPUG00000011619	1 retrocopy	retro_mputfur_280,
Mus musculus	ENSMUSG00000030216	1 retrocopy	retro_mmus_2740,
Nomascus leucogenys	ENSNLEG00000003926	1 retrocopy	retro_nleu_2651,
Oryctolagus cuniculus	ENSOCUG00000017177	1 retrocopy	retro_ocun_974,
Otolemur garnettii	ENSOGAG00000010518	1 retrocopy	retro_ogar_207,
Ochotona princeps	ENSOPRG00000015008	3 retrocopies	retro_opri_107, retro_opri_1159, retro_opri_678,
Pongo abelii	ENSPPYG00000004323	3 retrocopies	retro_pabe_1558 , retro_pabe_2099, retro_pabe_3663,
Pan troglodytes	ENSPTRG00000004724	3 retrocopies	retro_ptro_1260, retro_ptro_1637, retro_ptro_3136,
Rattus norvegicus	ENSRNOG00000005505	3 retrocopies	retro_rnor_1287, retro_rnor_2726, retro_rnor_741,
Rattus norvegicus	ENSRNOG00000049593	1 retrocopy	retro_rnor_740,
Sorex araneus	ENSSARG00000007085	1 retrocopy	retro_sara_753,
Sarcophilus harrisii	ENSSHAG00000016649	1 retrocopy	retro_shar_81,
Tupaia belangeri	ENSTBEG00000003394	1 retrocopy	retro_tbel_2213,