RetrogeneDB ID:

retro_lafr_1100

Retrocopy
location
Organism:Elephant (Loxodonta africana)
Coordinates:scaffold_7:64025946..64026330(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLAFG00000029861
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL22
Ensembl ID:ENSLAFG00000006352
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lafr_1100
ATGGCACCTGTGAAAAAACTTGTGGTGAAAGAGGGCAAAAAAAAAGAAGCAGGTTTTGAAGTTCACCCTTGACTGCACCC
ACCCTGTAGAAGATGGAATCACTGATGCTGCCAATTTTGAGCAGTTTCTTCAAGAAAGAACCAAAGTTAATGGGAAAGCT
GGTAATCTTGGTGGAGGGGTTGTAACCATTGAACGAAGCAAGAGCAAGATTACTGTAACCTCCGAGGTGCCTTTTTCCAA
AAGGTATTTGAAGTATTTCACCAAAAATATTTGAAGAAGAATAATCCACGTGATTGGTTGCGCGTGGTCGCTGACAGCAA
AGAAAGTTACGAATTACGTTACTTCCAAATTAACCAGGTTGAAGAAGAGGAAGAAGATGAGGAT

ORF - retro_lafr_1100 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.31 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAPVKKLVAKGGKKK-KQVLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGVVTIERSKSK
MAPVKKLV.K.GKKK.KQVLKFTLDCTHPVEDGI.DAANFEQFLQER.KVNGKAGNLGGGVVTIERSKSK
RetrocopyMAPVKKLVVKEGKKK>KQVLKFTLDCTHPVEDGITDAANFEQFLQERTKVNGKAGNLGGGVVTIERSKSK
ParentalITVTSEVPFSKRYLKYLTK-KYLKKNNLRDWLRVVANSKESYELRYFQINQDEEEEEDED
ITVTSEVPFSKRYLKY.TK.KYLKKNN.RDWLRVVA.SKESYELRYFQINQ.EEEEEDED
RetrocopyITVTSEVPFSKRYLKYFTK<KYLKKNNPRDWLRVVADSKESYELRYFQINQVEEEEEDED

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






RNA-Seq - click to see more details

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Loxodonta africana was not studied using ChIP-Seq data.

EST - click to see more details

Loxodonta africana was not studied using EST data.

TSS - click to see more details

Loxodonta africana was not studied using FANTOM5 data.

Lab - click to see more details

retro_lafr_1100 was not experimentally validated.

Retrocopy orthology:
Loxodonta africana 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 22 parental genes, and 185 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000098647 retrocopies
retro_amel_1219, retro_amel_1247, retro_amel_1775, retro_amel_1793, retro_amel_369, retro_amel_830, retro_amel_870,
Bos taurus ENSBTAG000000144234 retrocopies
retro_btau_1491, retro_btau_566, retro_btau_694, retro_btau_892,
Choloepus hoffmanni ENSCHOG000000074772 retrocopies
retro_chof_1785, retro_chof_2537,
Callithrix jacchus ENSCJAG0000000013212 retrocopies
retro_cjac_1032, retro_cjac_1055, retro_cjac_1257, retro_cjac_1301, retro_cjac_2352, retro_cjac_2436, retro_cjac_2874, retro_cjac_2954, retro_cjac_3925, retro_cjac_472, retro_cjac_611, retro_cjac_867,
Dasypus novemcinctus ENSDNOG000000131668 retrocopies
retro_dnov_1282, retro_dnov_1523, retro_dnov_2043, retro_dnov_2126, retro_dnov_38, retro_dnov_382, retro_dnov_425, retro_dnov_567,
Felis catus ENSFCAG000000063203 retrocopies
retro_fcat_1591, retro_fcat_1656, retro_fcat_1715,
Homo sapiens ENSG0000011625116 retrocopies
retro_hsap_1162, retro_hsap_1299, retro_hsap_1445, retro_hsap_1720, retro_hsap_2136, retro_hsap_2138, retro_hsap_2142, retro_hsap_2306, retro_hsap_2315, retro_hsap_349, retro_hsap_3814, retro_hsap_485, retro_hsap_4865, retro_hsap_4909, retro_hsap_600, retro_hsap_726,
Gorilla gorilla ENSGGOG0000002773910 retrocopies
retro_ggor_1111, retro_ggor_1652, retro_ggor_1655, retro_ggor_1708, retro_ggor_1757, retro_ggor_2268, retro_ggor_2567, retro_ggor_37, retro_ggor_531, retro_ggor_613,
Loxodonta africana ENSLAFG00000006352 5 retrocopies
retro_lafr_1100 , retro_lafr_380, retro_lafr_649, retro_lafr_981, retro_lafr_993,
Loxodonta africana ENSLAFG000000132202 retrocopies
retro_lafr_1121, retro_lafr_682,
Macaca mulatta ENSMMUG0000001834712 retrocopies
retro_mmul_1004, retro_mmul_1044, retro_mmul_1047, retro_mmul_1512, retro_mmul_2209, retro_mmul_2264, retro_mmul_2467, retro_mmul_2601, retro_mmul_271, retro_mmul_445, retro_mmul_469, retro_mmul_80,
Mustela putorius furoENSMPUG000000070876 retrocopies
retro_mputfur_1074, retro_mputfur_1277, retro_mputfur_134, retro_mputfur_1433, retro_mputfur_578, retro_mputfur_873,
Mus musculus ENSMUSG000000289365 retrocopies
retro_mmus_1883, retro_mmus_1906, retro_mmus_2123, retro_mmus_2459, retro_mmus_3171,
Nomascus leucogenys ENSNLEG0000001033710 retrocopies
retro_nleu_1309, retro_nleu_2354, retro_nleu_2367, retro_nleu_2509, retro_nleu_2747, retro_nleu_2772, retro_nleu_2783, retro_nleu_2881, retro_nleu_2946, retro_nleu_3003,
Otolemur garnettii ENSOGAG000000147767 retrocopies
retro_ogar_1116, retro_ogar_1415, retro_ogar_1418, retro_ogar_2188, retro_ogar_2979, retro_ogar_399, retro_ogar_917,
Pongo abelii ENSPPYG0000000195111 retrocopies
retro_pabe_1196, retro_pabe_1213, retro_pabe_1435, retro_pabe_166, retro_pabe_248, retro_pabe_3114, retro_pabe_349, retro_pabe_3782, retro_pabe_3817, retro_pabe_590, retro_pabe_966,
Pan troglodytes ENSPTRG0000000007614 retrocopies
retro_ptro_1562, retro_ptro_1563, retro_ptro_1630, retro_ptro_1690, retro_ptro_2596, retro_ptro_275, retro_ptro_3056, retro_ptro_3240, retro_ptro_365, retro_ptro_502, retro_ptro_517, retro_ptro_795, retro_ptro_950, retro_ptro_984,
Rattus norvegicus ENSRNOG000000111045 retrocopies
retro_rnor_1315, retro_rnor_1687, retro_rnor_2089, retro_rnor_2149, retro_rnor_439,
Sus scrofa ENSSSCG000000033674 retrocopies
retro_sscr_257, retro_sscr_276, retro_sscr_497, retro_sscr_509,
Tupaia belangeri ENSTBEG0000000917233 retrocopies
retro_tbel_1047, retro_tbel_1181, retro_tbel_1263, retro_tbel_1422, retro_tbel_1773, retro_tbel_1951, retro_tbel_2121, retro_tbel_2182, retro_tbel_2231, retro_tbel_2429, retro_tbel_2452, retro_tbel_2801, retro_tbel_2923, retro_tbel_3090, retro_tbel_3160, retro_tbel_3265, retro_tbel_3362, retro_tbel_3482, retro_tbel_3719, retro_tbel_3885, retro_tbel_3960, retro_tbel_397, retro_tbel_4199, retro_tbel_4225, retro_tbel_4386, retro_tbel_4437, retro_tbel_4607, retro_tbel_504, retro_tbel_582, retro_tbel_659, retro_tbel_680, retro_tbel_755, retro_tbel_920,
Tursiops truncatus ENSTTRG000000104888 retrocopies
retro_ttru_1268, retro_ttru_147, retro_ttru_1519, retro_ttru_1564, retro_ttru_1739, retro_ttru_413, retro_ttru_714, retro_ttru_871,
Vicugna pacos ENSVPAG000000094661 retrocopy
retro_vpac_330,


Copyright © RetrogeneDB 2014-2017