RetrogeneDB ID: retro_itri_299

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393283.1:7947862..7948378(+)
• Located in intron of: ENSSTOG00000007895

Retrocopy information

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

Parental gene information

• Parental gene symbol: BNIP3
• Ensembl ID: ENSSTOG00000012456
• Aliases: None
• Description: BCL2/adenovirus E1B 19kDa interacting protein 3 [Source:HGNC Symbol;Acc:1084]

Sequence

>retro_itri_299
GAGCTACACTTTAGCAATAATGGAAATGGGAGCAGTGCTTCAGTTTCAGTTTTTGTTTATAATGATGACATGGAAAAAAT
ACTGCCAGGTGCCCAGCATGAATCTGGGATGCAGTAGCTCCAAGAGTTCTCAATGAGAGACAGCCATCTCACTTATAGGC
ACCACTAGATACAAATAGAGCTTCTGAAACAGACACCCTTAGCATTAGAGAAAACAGCAGCTCTCAGTCCAAGAAAGATG
TTATTAAGGAAAGAAGCTGGAAGATCTTGAAGAAAAACTTAGATTGAATAAATGGCTGATCAAGTCATCTAAAAAAATAT
ATCTCCCCAAGGAGTTCCTCCTTAAATACCAGAAGTACACATCTACTCTCAGTATGAGAAACACCACACTAAAGAGAAAG
GAGCATCTTCTTGGTGAAATTTCTAAAGGTTTTTCATCTCTGCTGCTCTTTCCTCCACTGGCCATTGGCCCAGGAACTAT
GTTAGAAGGCATATAACAGCCTCCACCAGCACCTTT

Alignment

ORF - retro_itri_299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.78 %
• Parental protein coverage: 90.16 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ELHFSN-GNGSGVPASVSIYNGDMEKILLDAQHESGR-SSSKSSHCDS-PPRSQTPQENTRASETDAHSI
          ELHFSN.GNGS....SV..YN.DMEKIL..AQHESG..SSSKSS.....P.....P....RASETD..SI
Retrocopy ELHFSNNGNGSSASVSVFVYNDDMEKILPGAQHESGM>SSSKSSQ*ET>PSHL*APLDTNRASETDTLSI

Parental  GEKNSSQSEEDYLERRKEVESILKKNSDWIWDWSSRP-ENIPP-KEFLFRHPKRTATLSMRNTSVMKKGG
          .E..SSQS..D....R.....ILKKN.D.I...SS....NI.P.KEFL....K.T.TLSMRNT....K..
Retrocopy RENSSSQSKKDVIKERS--WKILKKNLD*ING*SSHL>KNISP>KEFLLKYQKYTSTLSMRNTTLKRKEH

Parental  IFSAEFLKVFLPSLLLSHLLAIGLGI-YIGRRLTTSTSTF
          ....E..K.F..SLLL...LAIG.G..Y..R..T.STSTF
Retrocopy LL-GEISKGF-SSLLLFPPLAIGPGT<YVRRHITASTSTF

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_299 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_299 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 147 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002150	2 retrocopies	retro_chof_1555, retro_chof_559,
Callithrix jacchus	ENSCJAG00000000228	8 retrocopies	retro_cjac_1882, retro_cjac_2068, retro_cjac_2105, retro_cjac_2106, retro_cjac_2107, retro_cjac_2108, retro_cjac_3953, retro_cjac_4031,
Cavia porcellus	ENSCPOG00000005882	7 retrocopies	retro_cpor_1138, retro_cpor_1283, retro_cpor_344, retro_cpor_376, retro_cpor_496, retro_cpor_600, retro_cpor_647,
Dipodomys ordii	ENSDORG00000012511	1 retrocopy	retro_dord_431,
Equus caballus	ENSECAG00000017458	3 retrocopies	retro_ecab_652, retro_ecab_921, retro_ecab_969,
Echinops telfairi	ENSETEG00000011704	1 retrocopy	retro_etel_1779,
Homo sapiens	ENSG00000176171	21 retrocopies	retro_hsap_1308, retro_hsap_1486, retro_hsap_1976, retro_hsap_1979, retro_hsap_1980, retro_hsap_1983, retro_hsap_1985, retro_hsap_1986, retro_hsap_1988, retro_hsap_1990, retro_hsap_2035, retro_hsap_2036, retro_hsap_2039, retro_hsap_2040, retro_hsap_2042, retro_hsap_2043, retro_hsap_2044, retro_hsap_2046, retro_hsap_3741, retro_hsap_3743, retro_hsap_3858,
Gorilla gorilla	ENSGGOG00000014520	17 retrocopies	retro_ggor_1138, retro_ggor_1433, retro_ggor_1434, retro_ggor_1436, retro_ggor_1437, retro_ggor_1438, retro_ggor_1439, retro_ggor_1440, retro_ggor_1466, retro_ggor_1467, retro_ggor_1468, retro_ggor_1469, retro_ggor_1472, retro_ggor_1474, retro_ggor_1475, retro_ggor_2521, retro_ggor_2599,
Microcebus murinus	ENSMICG00000011985	1 retrocopy	retro_mmur_563,
Macaca mulatta	ENSMMUG00000022445	13 retrocopies	retro_mmul_1367, retro_mmul_1369, retro_mmul_1371, retro_mmul_1392, retro_mmul_1393, retro_mmul_1394, retro_mmul_1681, retro_mmul_355, retro_mmul_421, retro_mmul_739, retro_mmul_754, retro_mmul_772, retro_mmul_819,
Mus musculus	ENSMUSG00000078566	4 retrocopies	retro_mmus_1194, retro_mmus_1195, retro_mmus_2207, retro_mmus_3577,
Nomascus leucogenys	ENSNLEG00000001613	26 retrocopies	retro_nleu_140, retro_nleu_1708, retro_nleu_2220, retro_nleu_2306, retro_nleu_2617, retro_nleu_2619, retro_nleu_2620, retro_nleu_2621, retro_nleu_2870, retro_nleu_2872, retro_nleu_2903, retro_nleu_2904, retro_nleu_2905, retro_nleu_2907, retro_nleu_2910, retro_nleu_2917, retro_nleu_2918, retro_nleu_2919, retro_nleu_2920, retro_nleu_2921, retro_nleu_2923, retro_nleu_2924, retro_nleu_2942, retro_nleu_3064, retro_nleu_3103, retro_nleu_3104,
Pongo abelii	ENSPPYG00000002771	18 retrocopies	retro_pabe_1629, retro_pabe_1631, retro_pabe_1632, retro_pabe_1633, retro_pabe_1665, retro_pabe_1666, retro_pabe_1667, retro_pabe_1670, retro_pabe_1688, retro_pabe_1694, retro_pabe_1703, retro_pabe_2499, retro_pabe_3049, retro_pabe_3050, retro_pabe_3120, retro_pabe_3122, retro_pabe_3533, retro_pabe_3569,
Pan troglodytes	ENSPTRG00000003067	17 retrocopies	retro_ptro_1005, retro_ptro_1317, retro_ptro_1319, retro_ptro_1323, retro_ptro_1324, retro_ptro_1325, retro_ptro_1327, retro_ptro_1353, retro_ptro_1354, retro_ptro_1356, retro_ptro_1357, retro_ptro_1359, retro_ptro_1360, retro_ptro_1361, retro_ptro_1363, retro_ptro_2629, retro_ptro_3062,
Rattus norvegicus	ENSRNOG00000017243	3 retrocopies	retro_rnor_1070, retro_rnor_2645, retro_rnor_2732,
Sus scrofa	ENSSSCG00000024388	1 retrocopy	retro_sscr_827,
Ictidomys tridecemlineatus	ENSSTOG00000004029	1 retrocopy	retro_itri_1525,
Ictidomys tridecemlineatus	ENSSTOG00000012456	1 retrocopy	retro_itri_299 ,
Tupaia belangeri	ENSTBEG00000000487	1 retrocopy	retro_tbel_2600,
Tursiops truncatus	ENSTTRG00000008038	1 retrocopy	retro_ttru_1538,