RetrogeneDB ID: retro_pmar_6

Retrocopy location

• Organism: Lamprey (Petromyzon marinus)
• Coordinates: GL499355:91..1036(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPMAG00000010232
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: rplp0 (1 of 2)
• Ensembl ID: ENSPMAG00000001339
• Aliases: None
• Description: ribosomal protein, large, P0 [Source:ZFIN;Acc:ZDB-GENE-000629-1]

Sequence

>retro_pmar_6
ATGCCCAGGGAAGACAAGTCAACTTGGAAGTCAAATTACTTCCTGAAGATCATCCAACTTCTGGAAGATTTCCCAAAATG
CTTCATCGTCGGCGCAGACAATGTCGGCTCCAAGCAGATGCAGCAGATCCGCATGTCGTTGCGTGGGAAAGCTGTGGTGC
TCATGGGCAAGAACACCATGATGCGCAAAGCCATCCGTGGTCACCTTGAGAAAAACCCAGCACTTGAGAGAGTGTTGCCA
TACATTCGCGGGAATGTTGGGTTTGTCTTCACCAAGGAGGACCTGGCTGAGATCCGTGACATGCTTCTTGCCAACAAGGT
CCCGGCCTCGGCACGCGCCGGAGGTCTGGCTCCATGCGACGTGATGGTGCCGGCACAGAACACCGGGCTCGGTCCTGAAA
AGACCTCCTTCTTCCAGGCTCTTGGCATCACCACCAAGATCTCAAGAGGCACCATTGAAATTCTGAGCGACGTGCAGCTG
ATCAAGGCGGGTGACAAGGTGGGGGCCAGCGAGGCGACGCTTCTCAACATGCTCAACATCTCGCCCTTCACCTTCGGGCT
CCACATCCTGCAGGTGTACGACAATGGCAGCATTTACAGCCCCGATGTGCTGGACATCACCGAGGATGACCTGCGCAAGC
GCTTCCTCGAGGGTGTGCGCAACGTCGCTAGCGTGTGCCTTCAGATTGGCTACCCGACCGTTGCCTCAATCCCACATTCC
ATCGTTAACGGCTACAAGCGTGTGCTCGCCATTGCCGTGGAGACCAACTACTCTTTCCCACTTGCCGACAAGGTTAAGGC
GTTCCTGGCTGACCCATCCGCCTTCGTGACAGCCGCACCTGTGGCAGCCGCGGCTGCGCCAGCTGCCGCTGCCAAGGAGG
AGAAGAAGCAGGAGTCTGAAGAGGAGGAGGAAGATGACGACATGGGTTTCGGTCTCTTTGACTAG

Alignment

ORF - retro_pmar_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 98.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDVQLIKAGDKVGASEATLLNMLNISPFTFGLHILQVYDNGSIYSPDVLDITEDDLRKRFLEGVRNVASV
          SDVQLIKAGDKVGASEATLLNMLNISPFTFGLHILQVYDNGSIYSPDVLDITEDDLRKRFLEGVRNVASV
Retrocopy SDVQLIKAGDKVGASEATLLNMLNISPFTFGLHILQVYDNGSIYSPDVLDITEDDLRKRFLEGVRNVASV

Parental  CLQIGYPTVASIPHSIVNGYKRVLAIAVETNYSFPLADKVKAFLADPSAFVTAAPVAAAAAPAAAAKEEK
          CLQIGYPTVASIPHSIVNGYKRVLAIAVETNYSFPLADKVKAFLADPSAFVTAAPVAAAAAPAAAAKEEK
Retrocopy CLQIGYPTVASIPHSIVNGYKRVLAIAVETNYSFPLADKVKAFLADPSAFVTAAPVAAAAAPAAAAKEEK

Parental  KQESEEEEEDDDMGFGLFD
          KQESEEEEEDDDMGFGLFD
Retrocopy KQESEEEEEDDDMGFGLFD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Petromyzon marinus was not studied using RNA-Seq expression data.

ChIP-Seq

Petromyzon marinus was not studied using ChIP-Seq data.

EST

7 EST(s) were mapped to retro_pmar_6 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CO546996	41	478	97.3	432	3	424
CO548919	46	430	95.9	379	4	369
DY252842	50	558	99.7	502	1	497
EE739724	57	558	99.9	500	1	499
FD703693	42	537	99.8	493	1	492
FD703708	42	546	99.5	501	3	498
FD728467	32	484	99.6	450	2	448

TSS

Petromyzon marinus was not studied using FANTOM5 data.

Lab

retro_pmar_6 was not experimentally validated.

Homology

Retrocopy orthology:

Petromyzon marinus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 30 parental genes, and 120 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003756	2 retrocopies	retro_acar_111, retro_acar_115,
Ailuropoda melanoleuca	ENSAMEG00000005144	4 retrocopies	retro_amel_1179, retro_amel_1194, retro_amel_1377, retro_amel_847,
Canis familiaris	ENSCAFG00000010227	5 retrocopies	retro_cfam_1580, retro_cfam_224, retro_cfam_487, retro_cfam_534, retro_cfam_693,
Choloepus hoffmanni	ENSCHOG00000002745	2 retrocopies	retro_chof_1115, retro_chof_2341,
Callithrix jacchus	ENSCJAG00000008677	3 retrocopies	retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Cavia porcellus	ENSCPOG00000021812	5 retrocopies	retro_cpor_298, retro_cpor_449, retro_cpor_475, retro_cpor_498, retro_cpor_601,
Equus caballus	ENSECAG00000015816	2 retrocopies	retro_ecab_1090, retro_ecab_585,
Erinaceus europaeus	ENSEEUG00000007553	1 retrocopy	retro_eeur_612,
Felis catus	ENSFCAG00000013354	1 retrocopy	retro_fcat_441,
Homo sapiens	ENSG00000089157	7 retrocopies	retro_hsap_1403, retro_hsap_1553, retro_hsap_1889, retro_hsap_2095, retro_hsap_2334, retro_hsap_512, retro_hsap_784,
Gorilla gorilla	ENSGGOG00000026582	5 retrocopies	retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Macropus eugenii	ENSMEUG00000016409	12 retrocopies	retro_meug_1211, retro_meug_1245, retro_meug_1339, retro_meug_1410, retro_meug_1672, retro_meug_1689, retro_meug_1789, retro_meug_1800, retro_meug_1943, retro_meug_2166, retro_meug_294, retro_meug_772,
Myotis lucifugus	ENSMLUG00000001970	11 retrocopies	retro_mluc_1016, retro_mluc_1460, retro_mluc_1503, retro_mluc_1806, retro_mluc_1966, retro_mluc_2293, retro_mluc_268, retro_mluc_497, retro_mluc_564, retro_mluc_565, retro_mluc_882,
Macaca mulatta	ENSMMUG00000009157	2 retrocopies	retro_mmul_2245, retro_mmul_939,
Mustela putorius furo	ENSMPUG00000003055	4 retrocopies	retro_mputfur_1632, retro_mputfur_362, retro_mputfur_426, retro_mputfur_910,
Mus musculus	ENSMUSG00000067274	2 retrocopies	retro_mmus_143, retro_mmus_2249,
Nomascus leucogenys	ENSNLEG00000000292	11 retrocopies	retro_nleu_1080, retro_nleu_1365, retro_nleu_1419, retro_nleu_1470, retro_nleu_1551, retro_nleu_1639, retro_nleu_1686, retro_nleu_1722, retro_nleu_2058, retro_nleu_2927, retro_nleu_3095,
Oryctolagus cuniculus	ENSOCUG00000005749	2 retrocopies	retro_ocun_293, retro_ocun_376,
Otolemur garnettii	ENSOGAG00000003843	4 retrocopies	retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Procavia capensis	ENSPCAG00000016429	6 retrocopies	retro_pcap_232, retro_pcap_314, retro_pcap_339, retro_pcap_353, retro_pcap_408, retro_pcap_67,
Petromyzon marinus	ENSPMAG00000001339	1 retrocopy	retro_pmar_6 ,
Pongo abelii	ENSPPYG00000005022	5 retrocopies	retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Pteropus vampyrus	ENSPVAG00000003110	3 retrocopies	retro_pvam_114, retro_pvam_62, retro_pvam_745,
Rattus norvegicus	ENSRNOG00000001148	3 retrocopies	retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii	ENSSHAG00000001623	2 retrocopies	retro_shar_286, retro_shar_413,
Ictidomys tridecemlineatus	ENSSTOG00000011327	4 retrocopies	retro_itri_1155, retro_itri_276, retro_itri_331, retro_itri_982,
Tupaia belangeri	ENSTBEG00000005498	1 retrocopy	retro_tbel_3323,
Tarsius syrichta	ENSTSYG00000009732	7 retrocopies	retro_tsyr_1133, retro_tsyr_130, retro_tsyr_1376, retro_tsyr_1429, retro_tsyr_727, retro_tsyr_75, retro_tsyr_84,
Tursiops truncatus	ENSTTRG00000005658	1 retrocopy	retro_ttru_965,
Vicugna pacos	ENSVPAG00000012156	2 retrocopies	retro_vpac_234, retro_vpac_45,