RetrogeneDB ID:

retro_itri_603

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393305.1:3251227..3251934(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSTOG00000010546
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_603
ATGGCCCCCAAACGCCAATCTTTGCTCCAGTCTCAAACAAAAAAACCCAAACTGCTTGCCGCCCCTGAGAAGGCGAATCC
ATCGGCCTCTCTGGGTTTGCCGAAGGGAGAAAAAGAAACAACAAGAAGCAATTGAACATATCAATGAAGTACAAAATGAA
ATAGACAGACTTAATGAACAAGCCAGTGAGGAGATATTGAAAGGAGAACAGAAATATAACAAACTCTGCCAACCATTTTT
TCAGAAGAGGTCAGAATTGATCACCAAAATCCCAAATTTTTGGGGTAACAACATTTGTCAACCACCCACAAGTGTCCGCA
CTGCTTGGGGAGGAAGATGAAGAGGCGCTGCATTATTTGACCAGAGCTGAAGTGACAGAATTTGAAGATATCAAATCAGG
TTACAGAATAGATTTTTATTTTGATGAAAATCCTTACTTCGAAAATAAAGTTCTCTCCAAAGAATTTCATCTGAATGAGA
GTGGTGATCCATCTTCAAAGTCCACTGAAATCAAATGGAAATCTGGAAAGGATTTGACAAAACGTTCAAGTCAAATGCAG
AATAAAGCCAGCAGGTAGAGGCAGCATAAAGAACCAGAGAGCTTCTTTACCTGGTTTACTGACCATTCTGATGCAGATGC
AGATGAGTTAGGAGAGGTCATCAAAGATGATATTTGGCCAAATCCATTGCAGTACTATTTGGTTCCT

ORF - retro_itri_603 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.31 %
Parental protein coverage: 83.45 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAPKRQSSLQSQTKKPKLPAAPEKANSSASLGLPKGEKE-QQEAIEHIDEVQNEIDRLNEQASEEILKVE
MAPKRQS.LQSQTKKPKL.AAPEKAN.SASLGLPKGEKE.QQEAIEHI.EVQNEIDRLNEQASEEILK.E
RetrocopyMAPKRQSLLQSQTKKPKLLAAPEKANPSASLGLPKGEKE>QQEAIEHINEVQNEIDRLNEQASEEILKGE
ParentalQKYNKLRQPFFQKRSELIAKIPNFW-VTTFVNHPQGLVSALLGEEDEEALHYLTRVEVTEFEDIKSGYRI
QKYNKL.QPFFQKRSELI.KIPNFW.VTTFVNHPQ..VSALLGEEDEEALHYLTR.EVTEFEDIKSGYRI
RetrocopyQKYNKLCQPFFQKRSELITKIPNFW>VTTFVNHPQ--VSALLGEEDEEALHYLTRAEVTEFEDIKSGYRI
ParentalDFYFDENPYFENKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRSSQTQNKASRKRQHEEPESFFTWFT
DFYFDENPYFENKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRSSQ.QNKASR.RQH.EPESFFTWFT
RetrocopyDFYFDENPYFENKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRSSQMQNKASR*RQHKEPESFFTWFT
ParentalDHSDAGADELGEVIKDDIWPNPLQYYLVP
DHSDA.ADELGEVIKDDIWPNPLQYYLVP
RetrocopyDHSDADADELGEVIKDDIWPNPLQYYLVP

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_603 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_603 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 21 parental genes, and 183 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000156867 retrocopies
retro_amel_1093, retro_amel_1201, retro_amel_1459, retro_amel_1675, retro_amel_530, retro_amel_631, retro_amel_634,
Bos taurus ENSBTAG000000209598 retrocopies
retro_btau_1179, retro_btau_1490, retro_btau_1519, retro_btau_1556, retro_btau_464, retro_btau_469, retro_btau_749, retro_btau_955,
Canis familiaris ENSCAFG000000327282 retrocopies
retro_cfam_47, retro_cfam_83,
Dasypus novemcinctus ENSDNOG000000028023 retrocopies
retro_dnov_160, retro_dnov_1830, retro_dnov_464,
Equus caballus ENSECAG000000091174 retrocopies
retro_ecab_358, retro_ecab_417, retro_ecab_505, retro_ecab_675,
Echinops telfairi ENSETEG0000001674615 retrocopies
retro_etel_1039, retro_etel_109, retro_etel_1123, retro_etel_1372, retro_etel_1649, retro_etel_1790, retro_etel_1872, retro_etel_1880, retro_etel_1930, retro_etel_1937, retro_etel_2110, retro_etel_2159, retro_etel_835, retro_etel_920, retro_etel_939,
Felis catus ENSFCAG000000058482 retrocopies
retro_fcat_130, retro_fcat_89,
Homo sapiens ENSG0000011933514 retrocopies
retro_hsap_1336, retro_hsap_1389, retro_hsap_1847, retro_hsap_241, retro_hsap_269, retro_hsap_2719, retro_hsap_2721, retro_hsap_3075, retro_hsap_3088, retro_hsap_3326, retro_hsap_3358, retro_hsap_420, retro_hsap_4722, retro_hsap_806,
Microcebus murinus ENSMICG000000176432 retrocopies
retro_mmur_1398, retro_mmur_775,
Myotis lucifugus ENSMLUG0000001429113 retrocopies
retro_mluc_1026, retro_mluc_1120, retro_mluc_1673, retro_mluc_1977, retro_mluc_2098, retro_mluc_2188, retro_mluc_2361, retro_mluc_2412, retro_mluc_2584, retro_mluc_419, retro_mluc_524, retro_mluc_855, retro_mluc_881,
Macaca mulatta ENSMMUG0000000853211 retrocopies
retro_mmul_1133, retro_mmul_1261, retro_mmul_1534, retro_mmul_2096, retro_mmul_2175, retro_mmul_2241, retro_mmul_2262, retro_mmul_2614, retro_mmul_362, retro_mmul_419, retro_mmul_569,
Mustela putorius furoENSMPUG0000001306910 retrocopies
retro_mputfur_1330, retro_mputfur_1556, retro_mputfur_1581, retro_mputfur_1605, retro_mputfur_221, retro_mputfur_274, retro_mputfur_286, retro_mputfur_723, retro_mputfur_785, retro_mputfur_799,
Mus musculus ENSMUSG0000005476617 retrocopies
retro_mmus_1366, retro_mmus_1435, retro_mmus_1671, retro_mmus_1743, retro_mmus_2329, retro_mmus_2448, retro_mmus_2484, retro_mmus_2664, retro_mmus_2665, retro_mmus_3015, retro_mmus_3290, retro_mmus_345, retro_mmus_3513, retro_mmus_517, retro_mmus_887, retro_mmus_929, retro_mmus_967,
Nomascus leucogenys ENSNLEG000000175952 retrocopies
retro_nleu_108, retro_nleu_870,
Oryctolagus cuniculus ENSOCUG0000000750112 retrocopies
retro_ocun_1107, retro_ocun_1110, retro_ocun_1234, retro_ocun_1311, retro_ocun_1563, retro_ocun_276, retro_ocun_407, retro_ocun_421, retro_ocun_423, retro_ocun_476, retro_ocun_859, retro_ocun_923,
Otolemur garnettii ENSOGAG0000000763513 retrocopies
retro_ogar_115, retro_ogar_1370, retro_ogar_3084, retro_ogar_3186, retro_ogar_3195, retro_ogar_3289, retro_ogar_447, retro_ogar_465, retro_ogar_543, retro_ogar_565, retro_ogar_806, retro_ogar_899, retro_ogar_934,
Pongo abelii ENSPPYG0000001965917 retrocopies
retro_pabe_1076, retro_pabe_1110, retro_pabe_1150, retro_pabe_1218, retro_pabe_1452, retro_pabe_1717, retro_pabe_1771, retro_pabe_2549, retro_pabe_2557, retro_pabe_2740, retro_pabe_299, retro_pabe_3667, retro_pabe_400, retro_pabe_414, retro_pabe_470, retro_pabe_720, retro_pabe_838,
Pan troglodytes ENSPTRG0000002143616 retrocopies
retro_ptro_1232, retro_ptro_1836, retro_ptro_1838, retro_ptro_2073, retro_ptro_2085, retro_ptro_209, retro_ptro_2151, retro_ptro_2152, retro_ptro_225, retro_ptro_2283, retro_ptro_2965, retro_ptro_3140, retro_ptro_321, retro_ptro_561, retro_ptro_913, retro_ptro_953,
Pteropus vampyrus ENSPVAG000000034372 retrocopies
retro_pvam_1198, retro_pvam_886,
Ictidomys tridecemlineatus ENSSTOG00000010546 6 retrocopies
retro_itri_1204, retro_itri_1588, retro_itri_477, retro_itri_529, retro_itri_603 , retro_itri_876,
Tursiops truncatus ENSTTRG000000116057 retrocopies
retro_ttru_1433, retro_ttru_1600, retro_ttru_181, retro_ttru_1901, retro_ttru_537, retro_ttru_919, retro_ttru_931,




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