RetrogeneDB ID:

retro_itri_1412

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393480.1:1389637..1390366(-)
Located in intron of:ENSSTOG00000000908
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL7
Ensembl ID:ENSSTOG00000004586
Aliases:None
Description:ribosomal protein L7 [Source:HGNC Symbol;Acc:10363]


Retrocopy-Parental alignment summary:






>retro_itri_1412
GAAAGAGAAGAGAAGGTTCCTGCTGTGCCAGAAACTCTTAAGAAAAAGTGAAGGAATTATGCAGAGTTGAAGGTAAAGTG
CCTGAGGAAGAAGTTTGCCCAAAAGATGCATAAAAAGGCAAGGAGGAAGCTTATCTATGAAAGAATCAAGCATTACCACT
AGGAATATAGGCAGATGTACTGAATAGGGATTCGAATGATTAGGATGGCAAAAAAAAGCTGGCAATTTCTATGTACTACA
GAATCCAAGTTGGCATTTGTCATTGGGATCAGAGGTACCAATGGTGTGAGCCCAAAGGTTTGTAAGGTATTACAACTTCT
TTGCCTTGGCCAGATCTTAATGGCACCTTCATTAAACTCAAGGAGGCCTCAATTAACATGCTGAGGAATTTGGAACCACA
TATGGAATGGGGGTACCCAAACCTGAAATCAGTGAATGAACTAATCTACAAGCGTGGATATGGCAAAATCAATAAGAAAC
AAATTGCCTTGATAGATAACACTTTGATTATTCCATGTGTTGATAAATATGGCATCATCTACATAGATGATCTGATTCAT
GAGATCTACACTGTTGGAAAACACTTCAAAGAAGCAAATAACTTCCTGTGGCCCTTCAAATTATCTTCTCCAAGAGTTGG
AATGAAGACAAAGATCACACATTTTTATAGGAGGTTGAGATGGTGGCAACAGGGAAGTCCAGATCAACAGGCTTATTAGA
AGGATGAAC

ORF - retro_itri_1412 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.52 %
Parental protein coverage: 97.98 %
Number of stop codons detected: 4
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalEKKKKVPAVPETLKKKRRNYAELKVKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMARMA
E...KVPAVPETLKKK.RNYAELKVK.LRKKFAQKM..KARRKLIYE..KHYH.EYRQMY...IRM.RM.
RetrocopyEREEKVPAVPETLKKK*RNYAELKVKCLRKKFAQKMHKKARRKLIYERIKHYH*EYRQMY*IGIRMIRMX
ParentalRK-AGNFYVPAEP-KLAFVIRIRGINGVSPKVRKVLQLLRLRQIF-NGTFVKLNKASINMLRIVEPYIAW
...AGNFYV...P.KLAFVI.IRG.NGVSPKV.KVLQLL.L.QI..NGTF.KL..ASINMLR..EP...W
RetrocopyXX>AGNFYVLQNP<KLAFVIGIRGTNGVSPKVCKVLQLLCLGQIL<NGTFIKLKEASINMLRNLEPHMEW
ParentalGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFK
GYPNLKSVNELIYKRGYGKINKK.IAL.DN.LI.....KYGII...DLIHEIYTVGK.FKEANNFLWPFK
RetrocopyGYPNLKSVNELIYKRGYGKINKKQIALIDNTLIIPCVDKYGIIYIDDLIHEIYTVGKHFKEANNFLWPFK
ParentalLSSPRGGMKKKTTH-FVEGGDAGNREDQINRLIRRMN
LSSPR.GMK.K.TH.F..G.D.GNRE.QINRLIRRMN
RetrocopyLSSPRVGMKTKITH>FIGG*DGGNREVQINRLIRRMN

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






RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_1412 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1412 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus 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 17 parental genes, and 237 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG0000002013922 retrocopies
retro_btau_1088, retro_btau_1231, retro_btau_1367, retro_btau_1381, retro_btau_1422, retro_btau_1434, retro_btau_1468, retro_btau_1548, retro_btau_1559, retro_btau_1616, retro_btau_1627, retro_btau_1784, retro_btau_1814, retro_btau_304, retro_btau_426, retro_btau_622, retro_btau_668, retro_btau_730, retro_btau_750, retro_btau_758, retro_btau_863, retro_btau_879,
Callithrix jacchus ENSCJAG000000076861 retrocopy
retro_cjac_105,
Equus caballus ENSECAG000000091881 retrocopy
retro_ecab_35,
Homo sapiens ENSG0000014760449 retrocopies
retro_hsap_1001, retro_hsap_1023, retro_hsap_1033, retro_hsap_1034, retro_hsap_1128, retro_hsap_113, retro_hsap_1232, retro_hsap_1281, retro_hsap_1614, retro_hsap_1626, retro_hsap_1844, retro_hsap_1862, retro_hsap_1957, retro_hsap_2008, retro_hsap_203, retro_hsap_2093, retro_hsap_2101, retro_hsap_2588, retro_hsap_2837, retro_hsap_3197, retro_hsap_3204, retro_hsap_3244, retro_hsap_3254, retro_hsap_3356, retro_hsap_3399, retro_hsap_344, retro_hsap_3453, retro_hsap_3493, retro_hsap_3560, retro_hsap_3573, retro_hsap_3625, retro_hsap_3717, retro_hsap_3775, retro_hsap_3883, retro_hsap_3918, retro_hsap_4137, retro_hsap_415, retro_hsap_426, retro_hsap_4306, retro_hsap_4662, retro_hsap_4704, retro_hsap_4718, retro_hsap_4761, retro_hsap_558, retro_hsap_616, retro_hsap_708, retro_hsap_729, retro_hsap_973, retro_hsap_976,
Latimeria chalumnae ENSLACG000000035711 retrocopy
retro_lcha_63,
Macropus eugenii ENSMEUG000000163199 retrocopies
retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Microcebus murinus ENSMICG000000028808 retrocopies
retro_mmur_1170, retro_mmur_1379, retro_mmur_139, retro_mmur_158, retro_mmur_52, retro_mmur_596, retro_mmur_646, retro_mmur_903,
Macaca mulatta ENSMMUG000000051411 retrocopy
retro_mmul_129,
Monodelphis domestica ENSMODG000000071364 retrocopies
retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Otolemur garnettii ENSOGAG000000039032 retrocopies
retro_ogar_15, retro_ogar_225,
Pongo abelii ENSPPYG0000001867150 retrocopies
retro_pabe_1025, retro_pabe_1061, retro_pabe_1087, retro_pabe_1326, retro_pabe_1454, retro_pabe_1520, retro_pabe_1642, retro_pabe_1677, retro_pabe_1908, retro_pabe_1998, retro_pabe_2004, retro_pabe_2118, retro_pabe_2197, retro_pabe_2348, retro_pabe_2656, retro_pabe_2690, retro_pabe_2762, retro_pabe_2796, retro_pabe_2807, retro_pabe_2808, retro_pabe_2856, retro_pabe_2886, retro_pabe_2936, retro_pabe_2946, retro_pabe_307, retro_pabe_3085, retro_pabe_3117, retro_pabe_3139, retro_pabe_3191, retro_pabe_3414, retro_pabe_3468, retro_pabe_3506, retro_pabe_352, retro_pabe_3622, retro_pabe_3651, retro_pabe_3662, retro_pabe_3669, retro_pabe_3675, retro_pabe_436, retro_pabe_497, retro_pabe_514, retro_pabe_551, retro_pabe_628, retro_pabe_655, retro_pabe_826, retro_pabe_844, retro_pabe_859, retro_pabe_865, retro_pabe_867, retro_pabe_933,
Rattus norvegicus ENSRNOG0000000699227 retrocopies
retro_rnor_1018, retro_rnor_1174, retro_rnor_1222, retro_rnor_1233, retro_rnor_1307, retro_rnor_1388, retro_rnor_1466, retro_rnor_1580, retro_rnor_1745, retro_rnor_1916, retro_rnor_1944, retro_rnor_2025, retro_rnor_2028, retro_rnor_2100, retro_rnor_2247, retro_rnor_2304, retro_rnor_2347, retro_rnor_2531, retro_rnor_2715, retro_rnor_2765, retro_rnor_2814, retro_rnor_2824, retro_rnor_530, retro_rnor_666, retro_rnor_911, retro_rnor_929, retro_rnor_977,
Ictidomys tridecemlineatus ENSSTOG00000004586 18 retrocopies
retro_itri_1025, retro_itri_1080, retro_itri_1358, retro_itri_1375, retro_itri_1412 , retro_itri_1430, retro_itri_1464, retro_itri_1593, retro_itri_1776, retro_itri_271, retro_itri_346, retro_itri_349, retro_itri_351, retro_itri_390, retro_itri_534, retro_itri_542, retro_itri_827, retro_itri_917,
Ictidomys tridecemlineatus ENSSTOG000000098412 retrocopies
retro_itri_1233, retro_itri_417,
Tupaia belangeri ENSTBEG000000023011 retrocopy
retro_tbel_2042,
Tarsius syrichta ENSTSYG0000000610025 retrocopies
retro_tsyr_1149, retro_tsyr_1200, retro_tsyr_1293, retro_tsyr_1297, retro_tsyr_1403, retro_tsyr_1598, retro_tsyr_1633, retro_tsyr_1850, retro_tsyr_1891, retro_tsyr_191, retro_tsyr_2109, retro_tsyr_2130, retro_tsyr_344, retro_tsyr_421, retro_tsyr_433, retro_tsyr_521, retro_tsyr_589, retro_tsyr_601, retro_tsyr_651, retro_tsyr_724, retro_tsyr_779, retro_tsyr_877, retro_tsyr_930, retro_tsyr_953, retro_tsyr_992,
Tursiops truncatus ENSTTRG0000000907416 retrocopies
retro_ttru_1241, retro_ttru_1546, retro_ttru_1690, retro_ttru_174, retro_ttru_1776, retro_ttru_1918, retro_ttru_210, retro_ttru_290, retro_ttru_367, retro_ttru_402, retro_ttru_534, retro_ttru_604, retro_ttru_726, retro_ttru_852, retro_ttru_933, retro_ttru_952,


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