RetrogeneDB ID: retro_hsap_88

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:25670336..25672232(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000151846
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PABPC1
• Ensembl ID: ENSG00000070756
• Aliases: PABPC1, PAB1, PABP, PABP1, PABPC2, PABPL1
• Description: poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]

Sequence

>retro_hsap_88
ATGAACCCCAGCACCCCCAGCTACCCAACGGCCTCGCTCTACGTGGGGGACCTCCACCCCGACGTGACTGAGGCGATGCT
CTACGAGAAGTTCAGCCCGGCAGGGCCCATCCTCTCCATCCGGATCTGCAGGGACTTGATCACCAGCGGCTCCTCCAACT
ACGCGTATGTGAACTTCCAGCATACGAAGGACGCGGAGCATGCTCTGGACACCATGAATTTTGATGTTATAAAGGGCAAG
CCAGTACGCATCATGTGGTCTCAGCGTGATCCATCACTTCGAAAAAGTGGAGTGGGCAACATATTCGTTAAAAATCTGGA
TAAGTCCATTAATAATAAAGCACTGTATGATACAGTTTCTGCTTTTGGTAACATCCTTTCGTGTAACGTGGTTTGTGATG
AAAATGGTTCCAAGGGTTATGGATTTGTACACTTTGAGACACACGAAGCAGCTGAAAGAGCTATTAAAAAAATGAACGGA
ATGCTCCTAAATGGTCGCAAAGTATTTGTTGGACAATTTAAGTCTCGTAAAGAACGAGAAGCTGAACTTGGAGCTAGGGC
AAAAGAGTTCCCCAATGTTTACATCAAGAATTTTGGAGAAGACATGGATGATGAGCGCCTTAAGGATCTCTTTGGCAAGT
TCGGGCCCGCCTTAAGTGTGAAAGTAATGACCGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGG
CATGAAGATGCACAGAAAGCTGTAGATGAGATGAATGGAAAGGAGCTCAATGGAAAACAAATTTACGTTGGTCGAGCTCA
GAAAAAAGTGGAACGGCAGACGGAACTTAAGCGCACATTTGAACAGATGAAGCAAGATAGGATCACCAGATACCAGGTTG
TTAATCTTTATGTGAAAAATCTTGATGATGGTATTGATGATGAACGTCTCCGGAAAGCGTTTTCTCCATTTGGTACAATC
ACTAGTGCAAAGGTTATGATGGAAGGTGGTCGCAGCAAAGGGTTTGGTTTTGTATGTTTCTCCTCCCCAGAAGAAGCCAC
TAAAGCAGTTACAGAAATGAACGGTAGAATTGTGGCCACAAAGCCATTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGC
GCCAGGCTTACCTCACTAACGAGTATATGCAGAGAATGGCAAGTGTACGAGCTGTGCCCAACCAGCGAGCACCTCCTTCA
GGTTACTTCATGACAGCTGTCCCACAGACTCAGAACCATGCTGCATACTATCCTCCTAGCCAAATTGCTCGACTAAGACC
AAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATCCATTCCAAAATAAGCCCAGTGCTATCCGCCCAGGTGCTCCTA
GAGTACCATTTAGTACTATGAGACCAGCTTCTTCACAGGTTCCACGAGTCATGTCAACGCAGCGTGTTGCTAACACATCA
ACACAGACAGTGGGTCCACGTCCTGCAGCTGCTGCTGCTGCTGCAGCTACCCCTGCTGTGCGCACGGTTCCACGGTATAA
ATATGCTGCGGGAGTTCGCAATCCTCAGCAACATCGTAATGCACAGCCACAAGTTACAATGCAACAGCTTGCTGTTCATG
TACAAGGTCAGGAAACTTTGACTGCCTCCAGGTTGGCATCTGCCCCTCCTCAAAAGCAAAAGCAAATGTTAGGTGAACGG
CTCTTTCCTCTTATTCAAGCCATGCACCCTACTCTTGCTGGGAAAATCACTGGCATGTTGTTGGAGATTGATAATTCAGA
ACTTCTTTATATGCTCGAGTCTCCAGAGTCACTCCGTTCTAAGGTTGATGAAGCTGTAGCTGTACTACAAGCCCACCAAG
CTAAAGAGGCTACCCAGAAAGCAGTTAACAGTGCTACCGGTGTTCCAACTGTTTAA

Alignment

ORF - retro_hsap_88 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.4 %
• Parental protein coverage: 61.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD
          MNPS.PSYP.ASLYVGDLHPDVTEAMLYEKFSPAGPILSIR.CRD.IT..S..YAYVNFQ...DAE.ALD
Retrocopy MNPSTPSYPTASLYVGDLHPDVTEAMLYEKFSPAGPILSIRICRDLITSGSSNYAYVNFQHTKDAEHALD

Parental  TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIF.KNLDKSI.NKALYDT.SAFGNILSC.VVCDENGSKGY
Retrocopy TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFVKNLDKSINNKALYDTVSAFGNILSCNVVCDENGSKGY

Parental  GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDL
          GFVHFET.EAAERAI.KMNGMLLN.RKVFVG.FKSRKEREAELGARAKEF.NVYIKNFGEDMDDERLKDL
Retrocopy GFVHFETHEAAERAIKKMNGMLLNGRKVFVGQFKSRKEREAELGARAKEFPNVYIKNFGEDMDDERLKDL

Parental  FGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF
          FGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKR.F
Retrocopy FGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRTF

Parental  EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
          EQMKQDRITRYQ.VNLYVKNLDDGIDDERLRK.FSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
Retrocopy EQMKQDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV

Parental  TEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPN
          TEMNGRIVATKPLYVALAQRKEERQA.LTN.YMQRMASVRAVPN
Retrocopy TEMNGRIVATKPLYVALAQRKEERQAYLTNEYMQRMASVRAVPN

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
bodymap2_adipose	0.26 RPM	940.21 RPM
bodymap2_adrenal	0.12 RPM	728.94 RPM
bodymap2_brain	0.33 RPM	156.20 RPM
bodymap2_breast	0.21 RPM	539.93 RPM
bodymap2_colon	0.08 RPM	1100.11 RPM
bodymap2_heart	0.04 RPM	176.04 RPM
bodymap2_kidney	0.17 RPM	326.71 RPM
bodymap2_liver	0.00 RPM	235.61 RPM
bodymap2_lung	0.12 RPM	1010.44 RPM
bodymap2_lymph_node	0.04 RPM	968.43 RPM
bodymap2_ovary	0.31 RPM	996.65 RPM
bodymap2_prostate	0.35 RPM	1375.63 RPM
bodymap2_skeletal_muscle	0.27 RPM	202.12 RPM
bodymap2_testis	59.29 RPM	1177.43 RPM
bodymap2_thyroid	0.32 RPM	400.84 RPM
bodymap2_white_blood_cells	0.33 RPM	2554.91 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_88 was not detected

EST

15 EST(s) were mapped to retro_hsap_88 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BG717008	25670297	25671008	99.1	707	3	701
BG718483	25670275	25671034	99.4	750	2	741
BI460001	25670162	25671090	98.5	791	8	776
BI464014	25670290	25670966	99.6	672	2	667
BI825788	25670331	25670947	99.7	613	1	610
BU567424	25670277	25670984	98.8	707	0	703
CD243801	25670318	25671120	97.7	796	5	783
CD358457	25670303	25671047	97.2	722	7	706
CD358574	25670199	25671120	99.2	818	0	808
CD358948	25670315	25671096	98.6	775	3	766
DB029258	25670309	25670915	100	606	0	606
DB032778	25670288	25670885	100	597	0	597
DB033450	25670410	25670980	100	570	0	570
DB039899	25670684	25671261	99.9	576	1	575
DB045095	25670387	25670943	99.5	556	0	555

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_32115	1660 libraries	150 libraries	15 libraries	0 libraries	4 libraries
TSS #2	TSS_32116	1825 libraries	2 libraries	2 libraries	0 libraries	0 libraries

The graphical summary, for retro_hsap_88 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_88 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_88 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_8
Pongo abelii	retro_pabe_68

---

Parental genes homology:

Parental genes homology involve 26 parental genes, and 51 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 ,
Homo sapiens	ENSG00000076067	1 retrocopy	retro_hsap_1143,
Homo sapiens	ENSG00000090621	2 retrocopies	retro_hsap_109, retro_hsap_74,
Homo sapiens	ENSG00000153250	1 retrocopy	retro_hsap_1131,
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	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,