RetrogeneDB ID: retro_pabe_1004

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:50430578..50431674(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000005376
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ST13
• Ensembl ID: ENSPPYG00000011858
• Aliases: ST13, FAM10A1
• Description: hsc70-interacting protein [Source:RefSeq peptide;Acc:NP_001127121]

Sequence

>retro_pabe_1004
ATGGACCCCCGCAAAGTGAACGAGCTTCGGACCTTTGTGAAAATGTGTAAGCAGGATCTGAGCGTTCTGCACACCGAGGA
AATGCGCTTCCTGAGGGAGTGGGTGGAGAGCATGGGAGGTACTGCTACTCAGAAAGCTGAATCAGAAGAAAATACCAAGG
AAGAAAAACCTGATAGTAAGAAGGTGGAGGAAGACTTAAAGGCAGACGAAGCATCAAGTGAGGAAAGTGATCTAGAAATT
GATAAAGAAGGTGTGATTGAACCAGACACTGATGCTCCTCAAGAAATGGGAGATGAAAATGCGGAGATAACAGGAGATGA
TGGATCAGGCAAATGATAAAAAAGTGGCTGCTATTGAAGCCCTAAATGATGGTGAACTCCAGAAAGCCATTGACTTATTC
ACAGATGCCATCAAGCTGACTCCCTGCTTGGCCATTTTGTATGCCAAGAGGGCCAGTGTCTTCGTCAAATTACAGAAGCC
AAATGCTGCCATCCGAGACTGTGACAGAGCCATTGAAATAAATCCTGATTCAGCTCAGCCTTACAAGAGGCGGGGGAAAG
CACACAGACTTCTAGGCCACTGGGAAGAAGCAGCCCATGATCTTGCCCTTGCCTGTAAATTGGATTATAATGAAGATGCT
AGTGCAATGCTGAAAGAAGTTCAACCTAGGGCACAGAAAATTGCAGAACATCAGAGAAAGTATGAGTGAAAACGTGAAGA
GCGAGAGATCAAAGAAAGAATAGAACGAGTTAAGAAGGCTCGAGAAGAGCATGAGAGAGCCCAGAGGGAGGAAGAAGCCA
GATGACAGTCAGGAGCTCAGTATGGCTCTTTTCCAGGTGGCTTTCCTGGGGGAATGCCTGGTAATTTTCCTGGAGGAATG
ACTGGAATGGGAGGGGGCATACCTGGAATGGCCGGAATGCCTGGACTCAATGAAATTCTTAGTGATCCAAAGGTTCTTGC
AGCCATGCGGGATCCAGAAGTTATGGTGGTCTTCCAGGATGTGGCTCAGAACCCAGCAAATATGTCAAAATACCAGAGCA
ACCCAAAGGTTATGAATCTCATCAGTAAATTGTCAGCCAAATTTGGAGGTCAAGCG

Alignment

ORF - retro_pabe_1004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.51 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDPRKVNELRAFVKMCKQDPSVLHTEEMRFLREWVESMGGKVPPATQKAKSEENTKEEKPDSKKVEEDLK
          MDPRKVNELR.FVKMCKQD.SVLHTEEMRFLREWVESMGG....ATQKA.SEENTKEEKPDSKKVEEDLK
Retrocopy MDPRKVNELRTFVKMCKQDLSVLHTEEMRFLREWVESMGGT---ATQKAESEENTKEEKPDSKKVEEDLK

Parental  ADEPSSEESDLEIDKEGVIEPDTDAPQEMGDENAEIT-EEMMDQANDKKVAAIEALNDGELQKAIDLFTD
          ADE.SSEESDLEIDKEGVIEPDTDAPQEMGDENAEIT.E.M.DQANDKKVAAIEALNDGELQKAIDLFTD
Retrocopy ADEASSEESDLEIDKEGVIEPDTDAPQEMGDENAEIT>EMM-DQANDKKVAAIEALNDGELQKAIDLFTD

Parental  AIKLNPRLAILYAKRASVFVKLQKPNAAIRDCDRAIEINPDSAQPYKWRGKAHRLLGHWEEAAHDLALAC
          AIKL.P.LAILYAKRASVFVKLQKPNAAIRDCDRAIEINPDSAQPYK.RGKAHRLLGHWEEAAHDLALAC
Retrocopy AIKLTPCLAILYAKRASVFVKLQKPNAAIRDCDRAIEINPDSAQPYKRRGKAHRLLGHWEEAAHDLALAC

Parental  KLDYDEDASAMLKEVQPRAQKIAEHRRKYERKREEREIKERIERVKKAREEHERAQREEEARRQSGAQYG
          KLDY.EDASAMLKEVQPRAQKIAEH.RKYE.KREEREIKERIERVKKAREEHERAQREEEAR.QSGAQYG
Retrocopy KLDYNEDASAMLKEVQPRAQKIAEHQRKYE*KREEREIKERIERVKKAREEHERAQREEEAR*QSGAQYG

Parental  SFPGGFPGGMPGNLPGGMPGMGGGMPGMAGMPGLNEILSDPEVLAAMQDPEVMVAFQDVAQNPANMSKYQ
          SFPGGFPGGMPGN.PGGM.GMGGG.PGMAGMPGLNEILSDP.VLAAM.DPEVMV.FQDVAQNPANMSKYQ
Retrocopy SFPGGFPGGMPGNFPGGMTGMGGGIPGMAGMPGLNEILSDPKVLAAMRDPEVMVVFQDVAQNPANMSKYQ

Parental  SNPKVMNLISKLSAKFGGQA
          SNPKVMNLISKLSAKFGGQA
Retrocopy SNPKVMNLISKLSAKFGGQA

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	0.06 RPM	61.04 RPM
SRP007412_cerebellum	0.00 RPM	67.12 RPM
SRP007412_heart	0.03 RPM	46.81 RPM
SRP007412_kidney	0.03 RPM	110.84 RPM
SRP007412_liver	0.00 RPM	56.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1004 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1004 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1004 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1203
Gorilla gorilla	retro_ggor_938

---

Parental genes homology:

Parental genes homology involve 26 parental genes, and 148 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005227	1 retrocopy	retro_acar_2,
Ailuropoda melanoleuca	ENSAMEG00000013880	1 retrocopy	retro_amel_135,
Bos taurus	ENSBTAG00000006202	4 retrocopies	retro_btau_254, retro_btau_427, retro_btau_621, retro_btau_658,
Canis familiaris	ENSCAFG00000001139	14 retrocopies	retro_cfam_1029, retro_cfam_1101, retro_cfam_1122, retro_cfam_1239, retro_cfam_1467, retro_cfam_1830, retro_cfam_1950, retro_cfam_1958, retro_cfam_247, retro_cfam_262, retro_cfam_582, retro_cfam_808, retro_cfam_901, retro_cfam_969,
Choloepus hoffmanni	ENSCHOG00000012676	1 retrocopy	retro_chof_2222,
Callithrix jacchus	ENSCJAG00000004644	11 retrocopies	retro_cjac_1843, retro_cjac_1953, retro_cjac_2177, retro_cjac_2275, retro_cjac_2789, retro_cjac_3123, retro_cjac_3570, retro_cjac_4019, retro_cjac_488, retro_cjac_640, retro_cjac_685,
Cavia porcellus	ENSCPOG00000002290	4 retrocopies	retro_cpor_1394, retro_cpor_1477, retro_cpor_166, retro_cpor_961,
Felis catus	ENSFCAG00000011847	2 retrocopies	retro_fcat_920, retro_fcat_987,
Homo sapiens	ENSG00000100380	16 retrocopies	retro_hsap_1055, retro_hsap_1203, retro_hsap_178, retro_hsap_201, retro_hsap_2078, retro_hsap_2189, retro_hsap_2853, retro_hsap_3206, retro_hsap_3907, retro_hsap_4009, retro_hsap_4876, retro_hsap_500, retro_hsap_619, retro_hsap_756, retro_hsap_812, retro_hsap_986,
Gorilla gorilla	ENSGGOG00000026747	16 retrocopies	retro_ggor_1600, retro_ggor_1734, retro_ggor_1791, retro_ggor_1975, retro_ggor_2177, retro_ggor_2634, retro_ggor_2692, retro_ggor_277, retro_ggor_3045, retro_ggor_629, retro_ggor_666, retro_ggor_749, retro_ggor_788, retro_ggor_832, retro_ggor_833, retro_ggor_938,
Microcebus murinus	ENSMICG00000008875	2 retrocopies	retro_mmur_481, retro_mmur_954,
Myotis lucifugus	ENSMLUG00000007764	2 retrocopies	retro_mluc_1088, retro_mluc_2021,
Macaca mulatta	ENSMMUG00000019118	3 retrocopies	retro_mmul_1842, retro_mmul_402, retro_mmul_438,
Monodelphis domestica	ENSMODG00000013042	2 retrocopies	retro_mdom_1087, retro_mdom_31,
Mustela putorius furo	ENSMPUG00000016432	15 retrocopies	retro_mputfur_1640, retro_mputfur_211, retro_mputfur_212, retro_mputfur_233, retro_mputfur_272, retro_mputfur_282, retro_mputfur_289, retro_mputfur_343, retro_mputfur_373, retro_mputfur_379, retro_mputfur_402, retro_mputfur_450, retro_mputfur_506, retro_mputfur_605, retro_mputfur_778,
Mus musculus	ENSMUSG00000022403	2 retrocopies	retro_mmus_2997, retro_mmus_651,
Nomascus leucogenys	ENSNLEG00000015378	17 retrocopies	retro_nleu_1142, retro_nleu_1155, retro_nleu_1606, retro_nleu_1852, retro_nleu_2075, retro_nleu_2088, retro_nleu_2376, retro_nleu_2404, retro_nleu_247, retro_nleu_2555, retro_nleu_2765, retro_nleu_3121, retro_nleu_3122, retro_nleu_319, retro_nleu_447, retro_nleu_552, retro_nleu_988,
Otolemur garnettii	ENSOGAG00000016932	1 retrocopy	retro_ogar_224,
Pongo abelii	ENSPPYG00000011858	14 retrocopies	retro_pabe_1004 , retro_pabe_2181, retro_pabe_2361, retro_pabe_2657, retro_pabe_2885, retro_pabe_3183, retro_pabe_3673, retro_pabe_3794, retro_pabe_437, retro_pabe_554, retro_pabe_727, retro_pabe_763, retro_pabe_798, retro_pabe_880,
Pelodiscus sinensis	ENSPSIG00000004553	1 retrocopy	retro_psin_42,
Pteropus vampyrus	ENSPVAG00000011908	2 retrocopies	retro_pvam_1104, retro_pvam_393,
Rattus norvegicus	ENSRNOG00000019070	8 retrocopies	retro_rnor_1360, retro_rnor_1725, retro_rnor_1798, retro_rnor_1976, retro_rnor_2204, retro_rnor_2372, retro_rnor_2481, retro_rnor_2543,
Sarcophilus harrisii	ENSSHAG00000000319	2 retrocopies	retro_shar_70, retro_shar_767,
Sus scrofa	ENSSSCG00000000071	1 retrocopy	retro_sscr_428,
Ictidomys tridecemlineatus	ENSSTOG00000003165	1 retrocopy	retro_itri_88,
Tursiops truncatus	ENSTTRG00000011510	5 retrocopies	retro_ttru_1245, retro_ttru_1425, retro_ttru_1615, retro_ttru_385, retro_ttru_670,