RetrogeneDB ID:

retro_pmar_23

Retrocopy
location
Organism:Lamprey (Petromyzon marinus)
Coordinates:GL495867:3036..3339(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPMAG00000001458
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:rpl5b
Ensembl ID:ENSPMAG00000002040
Aliases:None
Description:ribosomal protein L5b [Source:ZFIN;Acc:ZDB-GENE-040625-93]


Retrocopy-Parental alignment summary:






>retro_pmar_23
GAGCTCTCCAAGTAGGGCATCACCGCGGGACTCACCAACTACGCCGCCGCCTACCACACCGGCCTGCTGCTGACGCGGGG
CTCACGCGCACCACCACCGGCAACGAGGTGGTACGGCGCGCTCAAGGGCGCCGTCGTCGGGGGCCTCTCCATTGCCACAC
AGCCAAGCCAAGCGATTCCCGGGCTACGACTCGGAGAGAAAAAGAGTTCAACGCCGACGTCCAACCGCAAGTGCACCCTG
GGCACGTGAACGTGGCGGACTGCCATGCGTTCGCTCGTGGAGAACGACGAGGCCGCGTGCAAG

ORF - retro_pmar_23 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.14 %
Parental protein coverage: 53.93 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalELSKYGITVGLTNYAAAF--TCYLDAGLTRTTTGNKVFGALKGAVDGGLSI-PHS-TKRFPGYDSE-SKE
ELSK.GIT.GLTNYAAA......L..G...........GALKGAV.GGLSI.PHS..KRFPGYDSE..KE
RetrocopyELSK*GITAGLTNYAAAYHTGLLLTRGSRAPPPATRWYGALKGAVVGGLSI>PHSQAKRFPGYDSE>EKE
ParentalFNADVH-RKHILGVNVAD-YMRSLMENDEDAYK
FNADV....H...VNVAD..MRSL.ENDE.A.K
RetrocopyFNADVQPQVHPGHVNVAD>AMRSLVENDEAACK

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






RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Petromyzon marinus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pmar_23 retrocopy.

TSS - click to see more details

Petromyzon marinus was not studied using FANTOM5 data.

Lab - click to see more details

retro_pmar_23 was not experimentally validated.

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.
Parental genes homology:
Parental genes homology involve 33 parental genes, and 227 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098785 retrocopies
retro_amel_1200, retro_amel_137, retro_amel_139, retro_amel_1439, retro_amel_1669,
Bos taurus ENSBTAG000000020262 retrocopies
retro_btau_120, retro_btau_67,
Canis familiaris ENSCAFG000000201504 retrocopies
retro_cfam_1505, retro_cfam_1696, retro_cfam_905, retro_cfam_906,
Cavia porcellus ENSCPOG000000006988 retrocopies
retro_cpor_1047, retro_cpor_1097, retro_cpor_1141, retro_cpor_1259, retro_cpor_1354, retro_cpor_1387, retro_cpor_428, retro_cpor_737,
Dipodomys ordii ENSDORG000000056742 retrocopies
retro_dord_226, retro_dord_670,
Equus caballus ENSECAG000000210651 retrocopy
retro_ecab_654,
Erinaceus europaeus ENSEEUG000000028521 retrocopy
retro_eeur_620,
Echinops telfairi ENSETEG000000098898 retrocopies
retro_etel_1044, retro_etel_1089, retro_etel_1103, retro_etel_1264, retro_etel_2028, retro_etel_64, retro_etel_785, retro_etel_814,
Felis catus ENSFCAG000000246805 retrocopies
retro_fcat_281, retro_fcat_304, retro_fcat_453, retro_fcat_458, retro_fcat_463,
Homo sapiens ENSG0000012240630 retrocopies
retro_hsap_1266, retro_hsap_138, retro_hsap_1469, retro_hsap_1539, retro_hsap_1588, retro_hsap_1767, retro_hsap_183, retro_hsap_1989, retro_hsap_2143, retro_hsap_2385, retro_hsap_2594, retro_hsap_2600, retro_hsap_2777, retro_hsap_2962, retro_hsap_3105, retro_hsap_3178, retro_hsap_3181, retro_hsap_3209, retro_hsap_3430, retro_hsap_3520, retro_hsap_3941, retro_hsap_4048, retro_hsap_4104, retro_hsap_486, retro_hsap_590, retro_hsap_632, retro_hsap_646, retro_hsap_742, retro_hsap_780, retro_hsap_827,
Gorilla gorilla ENSGGOG0000000269924 retrocopies
retro_ggor_1129, retro_ggor_1172, retro_ggor_1206, retro_ggor_1342, retro_ggor_1343, retro_ggor_1656, retro_ggor_1934, retro_ggor_2052, retro_ggor_2130, retro_ggor_2178, retro_ggor_2243, retro_ggor_2318, retro_ggor_233, retro_ggor_2380, retro_ggor_264, retro_ggor_2649, retro_ggor_2715, retro_ggor_2755, retro_ggor_457, retro_ggor_521, retro_ggor_553, retro_ggor_622, retro_ggor_647, retro_ggor_996,
Loxodonta africana ENSLAFG000000119166 retrocopies
retro_lafr_1025, retro_lafr_1098, retro_lafr_302, retro_lafr_988, retro_lafr_989, retro_lafr_992,
Macropus eugenii ENSMEUG000000063613 retrocopies
retro_meug_1168, retro_meug_1537, retro_meug_2146,
Myotis lucifugus ENSMLUG000000089561 retrocopy
retro_mluc_925,
Monodelphis domestica ENSMODG000000116351 retrocopy
retro_mdom_748,
Mustela putorius furoENSMPUG000000041506 retrocopies
retro_mputfur_213, retro_mputfur_449, retro_mputfur_451, retro_mputfur_597, retro_mputfur_721, retro_mputfur_833,
Mus musculus ENSMUSG0000005855811 retrocopies
retro_mmus_1000, retro_mmus_1185, retro_mmus_1338, retro_mmus_1789, retro_mmus_1991, retro_mmus_2577, retro_mmus_2846, retro_mmus_297, retro_mmus_3076, retro_mmus_504, retro_mmus_911,
Nomascus leucogenys ENSNLEG000000105002 retrocopies
retro_nleu_2102, retro_nleu_39,
Ornithorhynchus anatinus ENSOANG000000046691 retrocopy
retro_oana_97,
Oryctolagus cuniculus ENSOCUG000000100892 retrocopies
retro_ocun_265, retro_ocun_54,
Otolemur garnettii ENSOGAG000000132466 retrocopies
retro_ogar_1164, retro_ogar_134, retro_ogar_1627, retro_ogar_2374, retro_ogar_2633, retro_ogar_707,
Procavia capensis ENSPCAG000000118652 retrocopies
retro_pcap_159, retro_pcap_201,
Petromyzon marinus ENSPMAG00000002040 1 retrocopy
retro_pmar_23 ,
Pongo abelii ENSPPYG0000000115232 retrocopies
retro_pabe_1053, retro_pabe_1219, retro_pabe_1274, retro_pabe_1307, retro_pabe_1331, retro_pabe_1501, retro_pabe_1918, retro_pabe_1931, retro_pabe_2019, retro_pabe_2123, retro_pabe_2238, retro_pabe_2457, retro_pabe_246, retro_pabe_247, retro_pabe_2640, retro_pabe_2641, retro_pabe_2658, retro_pabe_2813, retro_pabe_2841, retro_pabe_2909, retro_pabe_3247, retro_pabe_3320, retro_pabe_3360, retro_pabe_3534, retro_pabe_446, retro_pabe_447, retro_pabe_480, retro_pabe_51, retro_pabe_562, retro_pabe_572, retro_pabe_637, retro_pabe_740,
Pan troglodytes ENSPTRG0000000096330 retrocopies
retro_ptro_1038, retro_ptro_1068, retro_ptro_1184, retro_ptro_1326, retro_ptro_139, retro_ptro_1519, retro_ptro_1524, retro_ptro_1568, retro_ptro_169, retro_ptro_1744, retro_ptro_1878, retro_ptro_2005, retro_ptro_2241, retro_ptro_2262, retro_ptro_2264, retro_ptro_2329, retro_ptro_2391, retro_ptro_2674, retro_ptro_2742, retro_ptro_2785, retro_ptro_2941, retro_ptro_3027, retro_ptro_366, retro_ptro_433, retro_ptro_460, retro_ptro_470, retro_ptro_528, retro_ptro_577, retro_ptro_866, retro_ptro_997,
Pteropus vampyrus ENSPVAG000000151174 retrocopies
retro_pvam_1427, retro_pvam_355, retro_pvam_505, retro_pvam_527,
Rattus norvegicus ENSRNOG000000235296 retrocopies
retro_rnor_113, retro_rnor_2246, retro_rnor_2418, retro_rnor_2498, retro_rnor_2802, retro_rnor_2922,
Sarcophilus harrisii ENSSHAG000000064171 retrocopy
retro_shar_202,
Sus scrofa ENSSSCG000000068992 retrocopies
retro_sscr_149, retro_sscr_219,
Ictidomys tridecemlineatus ENSSTOG000000102562 retrocopies
retro_itri_1195, retro_itri_721,
Tupaia belangeri ENSTBEG000000105605 retrocopies
retro_tbel_101, retro_tbel_1054, retro_tbel_1518, retro_tbel_3006, retro_tbel_3530,
Tarsius syrichta ENSTSYG000000140388 retrocopies
retro_tsyr_1462, retro_tsyr_1548, retro_tsyr_206, retro_tsyr_248, retro_tsyr_670, retro_tsyr_737, retro_tsyr_786, retro_tsyr_952,
Tursiops truncatus ENSTTRG000000130975 retrocopies
retro_ttru_1446, retro_ttru_1548, retro_ttru_1796, retro_ttru_645, retro_ttru_979,




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