RetrogeneDB ID: retro_pabe_68

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:24259582..24261487(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000005219
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DKFZP469O2326
• Ensembl ID: ENSPPYG00000018790
• Aliases: DKFZP469O2326, PABPC1
• Description: polyadenylate-binding protein 1 [Source:RefSeq peptide;Acc:NP_001128842]

Sequence

>retro_pabe_68
ATGAACCCCAGCACCCCCAGCTACCCAACGGCCTCGCTCTACGTGGGGGACCTCCACCCCGACGTGACTGAGGCGATGCT
CTACGAGAAGTTCAGTCCGGCTGGGCCCATCCTTTCCATCCGGGTCTGCAGGGACTTGATCACCCGCCGCTCCTCCAACT
ACGCGTATGTGAACTTCCAGCACCCGAAGGACGCGGAGCATGCTCTGGACACCATGAATTTTGATGTTATAAAGGGCAAA
CCAGTACGCATCATGTGGTCTCAGCATGATCCATCACTTCGCAAAAGTGGAGTGGGCAACATATTCGTTAAAAATTTGGA
TAAATCCATTAATAATAAAGCACTGTATGATACAGTTTCTGCTTTTGGTAACATCCTTTCATGTAAGGTGGTTTGTGATG
AAAATGGTTCCAAGGGCTATGGATTTGTACACTTTGAGACACACGAAGCAGCTGAAAGAGCTATTGAAAAAATGAATGGA
ATGCTCCTAAATGATCGCAAAGTATTTGTTGGACGATTTAAGTCTCGTAAAGAACGAGAGGCTGAACTTGGAGCTAAGGC
AAAAGAGTTCCCCAATGTTTACATCAAGAATTTTGGAGAAGACATGGACGATGAGCGCCTTAAGGATCTCTTTGGCAAGT
TCGGGCCCGCCTTAAGTGTAAAAGTAATGACTGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAAG
CATGAAGATGCGCAGAAAGCTGTAGATGAGATGAATGGAAAGGAGCTCAGTGGAAAACAAATTTACGTTGGTCGAGCTCA
GAAAAAAGTGGAACGGCAGACGGAACTTAAGCGCAAATTTGAACAGATGAAGCAAGATAGGATCACCAGATACCAGGTTG
TTAATCTTTATGTGAAAAATCTTGATGATGATATTGATGATGAACGTCTCCGGAAAGCGTTTTCTCCATTTGGTACAATC
ACTAGTGCAAAGGTTATGATGGAAGGTGGTCGCAGCAAAGGGTTTGGTTTCGTATGTTTCTCTTCCCCAGAAGAAGCCAC
TAAAGCAGTTACAGAAATGAACGGTAGAATTGTGGCCACAAAGCCATTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGC
GCCAGGCTTACCTCACTAACGAGTATATGCAGAGAATGGCAAGTGTACGAGCTGTGCCCAACCCTGTAATCAACCCCTAC
CAGCCAGCACCTCCTTCAGGTTACTTCATGGCAGCTGTCCCACAGACTCAGAACCATGCTGCATACTATCCTCCTAGCCA
AATTGCTCAACTAAGACCAAGTCCTTGTTGGACTGCTCAGGGTGCCAGACCTCATCCATTCCAAAATAAGCCCAGTGCTA
TCTGCCCAGCTGCTCCTAGAGTACCGTTTAGTACTATGAGACCAGCTTCTTCACAGGTTCCACGAGTCATGTCAACGCAG
CGTGTTGCTAACACATCAACACAGACAGTGGGTCCACGTCCTGCAGCTGCTGCTGCTGCAGCTACCCCTGCTGTGCGCAC
GGTTCCACGGTATAAATATGCTGCGGGAGTTCGCAATCCTCAGCAACATCTTAATGCACAGCCGGAAGTTACAATGCAAC
AGCCTGCTGTTCATGTACAAGGTCAGGAAACTTTGACTGCTTCCATGTTGGCATCTGCCCCTCCTCAAAAGCAAAAGCAA
ATGTTGGGTGAACGGCTCTTTCCTCTTATTGAAGCCATGCGCCCTACTCTTGCTGGTAAAATCACTGGCATGTTGTTGGA
GATTGATAATTCAGAACTTCTTCATATGCTCGAGTCTCCAGAGTCACTCGGTTCTAAGGTTGATGAAGCTGTAGCTGTAC
TACAAGCCCACCAAGCTAAAGAGGCTACCCAGAAAGCAGTTAACAGTGCTACCGGTGTTCCAACT

Alignment

ORF - retro_pabe_68 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.02 %
• Parental protein coverage: 99.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD
          MNPS.PSYP.ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRD.ITRRS..YAYVNFQ.P.DAE.ALD
Retrocopy MNPSTPSYPTASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDLITRRSSNYAYVNFQHPKDAEHALD

Parental  TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          TMNFDVIKGKPVRIMWSQ.DPSLRKSGVGNIF.KNLDKSI.NKALYDT.SAFGNILSCKVVCDENGSKGY
Retrocopy TMNFDVIKGKPVRIMWSQHDPSLRKSGVGNIFVKNLDKSINNKALYDTVSAFGNILSCKVVCDENGSKGY

Parental  GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDL
          GFVHFET.EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGA.AKEF.NVYIKNFGEDMDDERLKDL
Retrocopy GFVHFETHEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFPNVYIKNFGEDMDDERLKDL

Parental  FGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF
          FGKFGPALSVKVMTDESGKSKGFGFVSFE.HEDAQKAVDEMNGKEL.GKQIYVGRAQKKVERQTELKRKF
Retrocopy FGKFGPALSVKVMTDESGKSKGFGFVSFEKHEDAQKAVDEMNGKELSGKQIYVGRAQKKVERQTELKRKF

Parental  EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
          EQMKQDRITRYQ.VNLYVKNLDD.IDDERLRK.FSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
Retrocopy EQMKQDRITRYQVVNLYVKNLDDDIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV

Parental  TEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRA
          TEMNGRIVATKPLYVALAQRKEERQA.LTN.YMQRMASVRAVPNPVINPYQPAPPSGYFMAA.PQTQN.A
Retrocopy TEMNGRIVATKPLYVALAQRKEERQAYLTNEYMQRMASVRAVPNPVINPYQPAPPSGYFMAAVPQTQNHA

Parental  AYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVANTSTQTM
          AYYPPSQIAQLRPSP.WTAQGARPHPFQN.P.AI.PAAPR.PFSTMRPASSQVPRVMSTQRVANTSTQT.
Retrocopy AYYPPSQIAQLRPSPCWTAQGARPHPFQNKPSAICPAAPRVPFSTMRPASSQVPRVMSTQRVANTSTQTV

Parental  GPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQ
          GPRPAAAAAAATPAVRTVP.YKYAAGVRNPQQHLNAQP.VTMQQPAVHVQGQE.LTASMLASAPPQ.QKQ
Retrocopy GPRPAAAAAAATPAVRTVPRYKYAAGVRNPQQHLNAQPEVTMQQPAVHVQGQETLTASMLASAPPQKQKQ

Parental  MLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAAQKAVNSA
          MLGERLFPLI.AM.PTLAGKITGMLLEIDNSELLHMLESPESL.SKVDEAVAVLQAHQAKEA.QKAVNSA
Retrocopy MLGERLFPLIEAMRPTLAGKITGMLLEIDNSELLHMLESPESLGSKVDEAVAVLQAHQAKEATQKAVNSA

Parental  TGVPT
          TGVPT
Retrocopy TGVPT

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	0.17 RPM	66.46 RPM
SRP007412_cerebellum	0.00 RPM	77.34 RPM
SRP007412_heart	0.09 RPM	75.41 RPM
SRP007412_kidney	0.03 RPM	161.86 RPM
SRP007412_liver	0.12 RPM	196.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_68 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_68 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_68 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_88
Pan troglodytes	retro_ptro_8

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000348	1 retrocopy	retro_amel_1650,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus	ENSCPOG00000012917	1 retrocopy	retro_cpor_1324,
Dasypus novemcinctus	ENSDNOG00000008718	2 retrocopies	retro_dnov_1530, retro_dnov_2259,
Felis catus	ENSFCAG00000001874	1 retrocopy	retro_fcat_1927,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Gorilla gorilla	ENSGGOG00000006785	1 retrocopy	retro_ggor_1986,
Myotis lucifugus	ENSMLUG00000012245	1 retrocopy	retro_mluc_579,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys	ENSNLEG00000003142	3 retrocopies	retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000001506	2 retrocopies	retro_pabe_190, retro_pabe_2563,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68 , retro_pabe_854,
Pteropus vampyrus	ENSPVAG00000016640	2 retrocopies	retro_pvam_10, retro_pvam_855,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Sus scrofa	ENSSSCG00000006063	2 retrocopies	retro_sscr_1153, retro_sscr_1205,
Ictidomys tridecemlineatus	ENSSTOG00000016395	2 retrocopies	retro_itri_139, retro_itri_48,
Tarsius syrichta	ENSTSYG00000004229	2 retrocopies	retro_tsyr_1743, retro_tsyr_273,
Tursiops truncatus	ENSTTRG00000004689	2 retrocopies	retro_ttru_1050, retro_ttru_1812,
Vicugna pacos	ENSVPAG00000003865	4 retrocopies	retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,