RetrogeneDB ID:

retro_etel_830

Retrocopy
location
Organism:Lesser hedgehog tenrec (Echinops telfairi)
Coordinates:scaffold_171796:149..1488(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSETEG00000018478
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSETEG00000004236
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_etel_830
GTCATTGGACACGTCGATTCTGGCAAGTCCACCACAACTGGTCACCTGATCTACAAATGTGGTGGGATCGACAAGAGAAC
CATCGAAAAGTCCGAGAAGGAAGCTGCTGAGATGGGAAAGGGCTCCTTCAAGTGTGCCTGGGTCTTGGATACGCTGAAAG
CCGAACGGGAACGTGGCATCACCACTGATATTTCCCCGTGGAAATTTGAGACCAGCAAGTACTATGTGACCATCATCGAT
GCCCCCAGACACAGAGACTTCATTAAAAACATGATGACAGGAACATCACAGGCTGACTGTGCTGTCCTCATCGTTGCTGC
TGGTGTGGGTGAATTTGAAGCTGGTATTTCCAAGAACGGGTAGACCCGTGAGCATGCCCTTCTGGCTTACACACTGGGTG
TGAAACAGCTCATTGTTGGTGTTAACAAAATGGAGTCTACTGAGCCACCCTACAGCCAGAAGAGATACGAGGAAATTGTT
AAGGAAGTCAGCACCTACATTAAGAAAATTGGCTACAACCCTGACACAGTAGCATTTGTGCCAATTTCTGGTTGGAATGG
TGACAACATGCTGGAACCAAGTGCTAATATGCCTTGGTTCAAGGGGTGGAAGGTGACCCGTAAGGATGGCAATGCCAGTG
GGACCACACTACTTGAAGCTCTGGATTGCATCCTGCCACCAACCCGCCCACCTGACAAGCCCCTGCGCCTCCCTCTCCAG
GACATCTACAAGATTGGTGGTATCGGGACTGTCCCTGTGGGCAGAGTGGAAACTGGGGTTCTGAAACCCGGTATGGTGGT
CACCTTTGCTCCAGTCAATGTTACCAATGTTGAAATGCACCACGAAGCTCTGAGTGAAGCTCTGCCTGGGGACAATGTCG
GGTTCAATGTCAAGAACGTCTCTGTCAAAGATGTTCGCCGTGGCAATGTGGCTGGTGACAGCAAAAATGACCCACCAATG
GAAGCAGCTGGCTTCACCGCTCAGGTGATCATCCTGAACCATCCAGGCCACGTCAATGCTGGATACGCACCTGTGCTGGA
TTGCCACACTGCCCACATTGCTTGCAAGTTTGCTGAGCTCAAAGAGAAGATTGATCGCCGTTCTGGCAAGAAGTTGGAAG
ATGGCCCCAAATTCTTGAAGTCTGGTGATGCTGCCATGGTTGACATGGTGCCTGGAAGCCCACGTGTGTGGAGAGCTTCT
CTGACTGTCCTCCTCTGGTCGCTTTGCTGTCCGAGACATGAGACAGGCCGTTGCTGTGAGCGTCATCAAGGCTGTGGACA
CAAAGGCTGCTGGAGCTGGCGAGGTCACCCAGTCTGCCCAGAAGGCTCAGAAGGCTAAA

ORF - retro_etel_830 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.6 %
Parental protein coverage: 97.62 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGITIDISLWKFE
VIGHVDSGKSTTTGHLIYKCGGIDKRTIEK.EKEAAEMGKGSFK.AWVLD.LKAERERGIT.DIS.WKFE
RetrocopyVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKSEKEAAEMGKGSFKCAWVLDTLKAERERGITTDISPWKFE
ParentalTSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLAYTLGVKQLIVG
TSKYYVTIIDAP.HRDFIKNM.TGTSQADCAVLIVAAGVGEFEAGISKNG.TREHALLAYTLGVKQLIVG
RetrocopyTSKYYVTIIDAPRHRDFIKNMMTGTSQADCAVLIVAAGVGEFEAGISKNG*TREHALLAYTLGVKQLIVG
ParentalVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPWFKGWKVTRKDG
VNKM.STEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPWFKGWKVTRKDG
RetrocopyVNKMESTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPWFKGWKVTRKDG
ParentalNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPVNVTTEVKS
NASGTTLLEALDCILPPTRP.DKPLRLPLQD.YKIGGIGTVPVGRVETGVLKPGMVVTFAPVNVT.....
RetrocopyNASGTTLLEALDCILPPTRPPDKPLRLPLQDIYKIGGIGTVPVGRVETGVLKPGMVVTFAPVNVT----N
ParentalVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVL
VEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPG...AGYAPVL
RetrocopyVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGHVNAGYAPVL
ParentalDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPG-KPMCVESFSDYPPL-GRFAVRDM
DCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAA.VDMVPG.KP.CVESFSD.PPL.GRFAVRDM
RetrocopyDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAMVDMVPG<KPTCVESFSDCPPL<GRFAVRDM
ParentalRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
RQ.VAV.VIKAVD.KAAGAG.VT.SAQKAQKAK
RetrocopyRQAVAVSVIKAVDTKAAGAGEVTQSAQKAQKAK

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






RNA-Seq - click to see more details

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Echinops telfairi was not studied using ChIP-Seq data.

EST - click to see more details

Echinops telfairi was not studied using EST data.

TSS - click to see more details

Echinops telfairi was not studied using FANTOM5 data.

Lab - click to see more details

retro_etel_830 was not experimentally validated.

Retrocopy orthology:
Echinops telfairi 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 15 parental genes, and 148 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000132491 retrocopy
retro_cfam_1007,
Dipodomys ordii ENSDORG000000096291 retrocopy
retro_dord_509,
Equus caballus ENSECAG000000222601 retrocopy
retro_ecab_802,
Erinaceus europaeus ENSEEUG000000003423 retrocopies
retro_eeur_407, retro_eeur_492, retro_eeur_625,
Echinops telfairi ENSETEG00000004236 14 retrocopies
retro_etel_1189, retro_etel_1248, retro_etel_1260, retro_etel_1429, retro_etel_1436, retro_etel_1472, retro_etel_1578, retro_etel_1602, retro_etel_1682, retro_etel_1808, retro_etel_2135, retro_etel_366, retro_etel_411, retro_etel_830 ,
Gorilla gorilla ENSGGOG0000002567520 retrocopies
retro_ggor_1193, retro_ggor_1258, retro_ggor_1305, retro_ggor_1444, retro_ggor_1529, retro_ggor_20, retro_ggor_2006, retro_ggor_2021, retro_ggor_2056, retro_ggor_2066, retro_ggor_2205, retro_ggor_2526, retro_ggor_2637, retro_ggor_2826, retro_ggor_322, retro_ggor_375, retro_ggor_790, retro_ggor_860, retro_ggor_919, retro_ggor_978,
Loxodonta africana ENSLAFG000000280811 retrocopy
retro_lafr_651,
Microcebus murinus ENSMICG0000001531921 retrocopies
retro_mmur_1027, retro_mmur_1116, retro_mmur_1145, retro_mmur_1182, retro_mmur_1190, retro_mmur_12, retro_mmur_1282, retro_mmur_1316, retro_mmur_1339, retro_mmur_1343, retro_mmur_1350, retro_mmur_1568, retro_mmur_171, retro_mmur_26, retro_mmur_273, retro_mmur_49, retro_mmur_682, retro_mmur_729, retro_mmur_825, retro_mmur_877, retro_mmur_9,
Monodelphis domestica ENSMODG000000185334 retrocopies
retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus ENSMUSG0000003774215 retrocopies
retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Otolemur garnettii ENSOGAG0000000915210 retrocopies
retro_ogar_1215, retro_ogar_1622, retro_ogar_1779, retro_ogar_1840, retro_ogar_2281, retro_ogar_2526, retro_ogar_2557, retro_ogar_3013, retro_ogar_3046, retro_ogar_3271,
Pongo abelii ENSPPYG000000167771 retrocopy
retro_pabe_12,
Ictidomys tridecemlineatus ENSSTOG000000076874 retrocopies
retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Tupaia belangeri ENSTBEG0000001215151 retrocopies
retro_tbel_1084, retro_tbel_1330, retro_tbel_1373, retro_tbel_1452, retro_tbel_166, retro_tbel_1841, retro_tbel_1969, retro_tbel_1994, retro_tbel_2088, retro_tbel_2091, retro_tbel_2179, retro_tbel_2205, retro_tbel_2206, retro_tbel_2218, retro_tbel_2232, retro_tbel_2419, retro_tbel_2505, retro_tbel_259, retro_tbel_2627, retro_tbel_2718, retro_tbel_2738, retro_tbel_2758, retro_tbel_282, retro_tbel_2976, retro_tbel_3032, retro_tbel_3065, retro_tbel_3067, retro_tbel_3281, retro_tbel_3307, retro_tbel_3315, retro_tbel_338, retro_tbel_354, retro_tbel_360, retro_tbel_372, retro_tbel_3813, retro_tbel_3865, retro_tbel_3967, retro_tbel_4125, retro_tbel_4192, retro_tbel_4282, retro_tbel_4352, retro_tbel_4370, retro_tbel_4466, retro_tbel_4496, retro_tbel_4639, retro_tbel_4660, retro_tbel_4695, retro_tbel_473, retro_tbel_588, retro_tbel_620, retro_tbel_903,
Drosophila melanogaster FBgn00005571 retrocopy
retro_dmel_9,


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