RetrogeneDB ID: retro_ptro_1987

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:52975629..52976255(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL7L1
• Ensembl ID: ENSPTRG00000018175
• Aliases: None
• Description: None

Sequence

>retro_ptro_1987
CAAAGAAGGAGCAAAGGAAAAGAGCTCAGGTTTAAGCGACTGGAATCATTCCAACATGATTCCTGGTGGCAGAAACATGA
CAAGCTGCTTCTCAGACAACTAGAAGTGAAACCTCATGCCTTGGAATTGCCAGATGAACATTCCTTGGCCTTTGTTGTGT
GCATCAAAAGGATTGATGGTGTGAGTTTACTGGGGCAGAGAACCATTGCAAGACTTCGCCTAAAGAAAATTTTTAATGGT
GTCTTTGTAAAAGCCACCCCCAAGAACCTAAAAATGCTGCGTATAGTGGAACCTTATGTGACCTAGGGATTTCCAAATCT
GAAGTCTGTCCAGGAATTTTGAATTTTGAAACGTGGACAAGCCAAGGTCAAGAATAAGACCATCTCTCTGACAGAAAACA
CAGTGATTGAGGAGCACCTGGGGAAGTTTGGTGTCATTTGCTTGGAAGACCTCATTCATGAAATTGCCTTCCCAGGGAAG
CATTTCCAGAGAGCTCATGGTTCTTGTGCCCTTTCCACCACTCAGTGGCCCGTCATGCTACCAAAAATAGAGTGGGCTTC
CTCAAGGAGATGGGCACAGCTGGCTATCAGGGTGAATGCATCAATCAGCTCATCCGCCAGCTGAAC

Alignment

ORF - retro_ptro_1987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.24 %
• Parental protein coverage: 84.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KEQKKGKGLRFKRLESFLHDSWRQKRDKVRLRRLEVKPHALELPDKHSLAFVVRIERIDGVSLLVQRTIA
          ....KGK.LRFKRLESF.HDSW.QK.DK..LR.LEVKPHALELPD.HSLAFVV.I.RIDGVSLL.QRTIA
Retrocopy QRRSKGKELRFKRLESFQHDSWWQKHDKLLLRQLEVKPHALELPDEHSLAFVVCIKRIDGVSLLGQRTIA

Parental  RLRLKKIFSGVFVKVTPQNLKMLRIVEPYVTWGFPNLKSVREL-ILKRGQAKVKNKTIPLTDNTVIEEHL
          RLRLKKIF.GVFVK.TP.NLKMLRIVEPYVT.GFPNLKSV.E..ILKRGQAKVKNKTI.LT.NTVIEEHL
Retrocopy RLRLKKIFNGVFVKATPKNLKMLRIVEPYVT*GFPNLKSVQEF*ILKRGQAKVKNKTISLTENTVIEEHL

Parental  GKFGVICLEDLIHEIAFPGKHFQ-EISWFLHPFHLSVARHATKNRVGFLKEMGTPGYRGERINQLIRQLN
          GKFGVICLEDLIHEIAFPGKHFQ.E.SWFL.PFH.SVARHATKNRVGFLKEMGT.GY.GE.INQLIRQLN
Retrocopy GKFGVICLEDLIHEIAFPGKHFQ<ESSWFLCPFHHSVARHATKNRVGFLKEMGTAGYQGECINQLIRQLN

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	0.02 RPM	15.94 RPM
SRP007412_cerebellum	0.00 RPM	11.15 RPM
SRP007412_heart	0.09 RPM	6.56 RPM
SRP007412_kidney	0.08 RPM	10.80 RPM
SRP007412_liver	0.03 RPM	6.84 RPM
SRP007412_testis	0.00 RPM	2.42 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1987 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1987 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3053
Gorilla gorilla	retro_ggor_2099
Pongo abelii	retro_pabe_2527

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 116 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012791	2 retrocopies	retro_amel_1260, retro_amel_243,
Bos taurus	ENSBTAG00000018478	2 retrocopies	retro_btau_588, retro_btau_816,
Canis familiaris	ENSCAFG00000001728	4 retrocopies	retro_cfam_1180, retro_cfam_1464, retro_cfam_1638, retro_cfam_330,
Choloepus hoffmanni	ENSCHOG00000000306	4 retrocopies	retro_chof_1168, retro_chof_1404, retro_chof_388, retro_chof_478,
Cavia porcellus	ENSCPOG00000021189	2 retrocopies	retro_cpor_1134, retro_cpor_653,
Dasypus novemcinctus	ENSDNOG00000013485	1 retrocopy	retro_dnov_689,
Equus caballus	ENSECAG00000003113	1 retrocopy	retro_ecab_998,
Erinaceus europaeus	ENSEEUG00000010431	1 retrocopy	retro_eeur_90,
Echinops telfairi	ENSETEG00000002419	3 retrocopies	retro_etel_1151, retro_etel_1823, retro_etel_542,
Felis catus	ENSFCAG00000009707	1 retrocopy	retro_fcat_143,
Homo sapiens	ENSG00000146223	22 retrocopies	retro_hsap_1285, retro_hsap_1291, retro_hsap_1602, retro_hsap_1623, retro_hsap_1661, retro_hsap_1836, retro_hsap_2201, retro_hsap_2389, retro_hsap_2735, retro_hsap_2845, retro_hsap_3053, retro_hsap_3068, retro_hsap_3077, retro_hsap_3187, retro_hsap_3250, retro_hsap_3373, retro_hsap_3556, retro_hsap_3641, retro_hsap_3846, retro_hsap_3957, retro_hsap_4770, retro_hsap_4827,
Monodelphis domestica	ENSMODG00000019028	1 retrocopy	retro_mdom_1708,
Mustela putorius furo	ENSMPUG00000013296	1 retrocopy	retro_mputfur_1577,
Mus musculus	ENSMUSG00000063888	4 retrocopies	retro_mmus_2359, retro_mmus_3172, retro_mmus_3626, retro_mmus_777,
Nomascus leucogenys	ENSNLEG00000004649	21 retrocopies	retro_nleu_1375, retro_nleu_1597, retro_nleu_1646, retro_nleu_1661, retro_nleu_2007, retro_nleu_2011, retro_nleu_2017, retro_nleu_2138, retro_nleu_2201, retro_nleu_2282, retro_nleu_2562, retro_nleu_2599, retro_nleu_2694, retro_nleu_2863, retro_nleu_2938, retro_nleu_332, retro_nleu_502, retro_nleu_536, retro_nleu_597, retro_nleu_711, retro_nleu_727,
Otolemur garnettii	ENSOGAG00000012671	3 retrocopies	retro_ogar_1380, retro_ogar_3358, retro_ogar_3428,
Pan troglodytes	ENSPTRG00000018175	23 retrocopies	retro_ptro_1074, retro_ptro_1088, retro_ptro_1127, retro_ptro_1162, retro_ptro_1671, retro_ptro_1849, retro_ptro_1927, retro_ptro_1987 , retro_ptro_2069, retro_ptro_2076, retro_ptro_2198, retro_ptro_2257, retro_ptro_2293, retro_ptro_2416, retro_ptro_2466, retro_ptro_2622, retro_ptro_2686, retro_ptro_2916, retro_ptro_2933, retro_ptro_3212, retro_ptro_355, retro_ptro_878, retro_ptro_882,
Pteropus vampyrus	ENSPVAG00000008696	3 retrocopies	retro_pvam_1179, retro_pvam_1482, retro_pvam_975,
Rattus norvegicus	ENSRNOG00000016269	1 retrocopy	retro_rnor_2795,
Sorex araneus	ENSSARG00000005286	2 retrocopies	retro_sara_100, retro_sara_211,
Sarcophilus harrisii	ENSSHAG00000011219	1 retrocopy	retro_shar_216,
Sus scrofa	ENSSSCG00000026472	3 retrocopies	retro_sscr_198, retro_sscr_756, retro_sscr_807,
Ictidomys tridecemlineatus	ENSSTOG00000009841	2 retrocopies	retro_itri_1233, retro_itri_417,
Tursiops truncatus	ENSTTRG00000006971	6 retrocopies	retro_ttru_1194, retro_ttru_171, retro_ttru_361, retro_ttru_498, retro_ttru_528, retro_ttru_915,
Vicugna pacos	ENSVPAG00000008894	2 retrocopies	retro_vpac_386, retro_vpac_584,