RetrogeneDB ID:

retro_itri_1274

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393422.1:4258337..4259631(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000026525
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TCP1
Ensembl ID:ENSSTOG00000005572
Aliases:None
Description:t-complex 1 [Source:HGNC Symbol;Acc:11655]


Retrocopy-Parental alignment summary:






>retro_itri_1274
TGCAAGGAAGCAGTGCGCTATATCAGTGAAAACTTAATTATTAACACAGATGAACTTGGAAGAGATTGCCTGATTAATGC
TGCCAAGACTTCCATGTCTTCCAAAATTATTGGAATAGATGGTGATTTCTTCTCTAATATGGTAGTAGATGCTGTACTTG
CTATTAAATACACAGATATAAGAGGCCAGCCTCGCTATCCTATCAATTCTGTTAATATTCTGAAAGCCCATGGGAGGAGT
CAGATGGAGAGCATGCTGATCAGTGGCTATGCACTTAACTATGTGGTGGGATCTCAGGGCATGCCCAAGAGAATAGTTAA
TGCAAAAGTTGCTTGCCTTGACTTCAGCCTACAGAAAACAAAAATGAAGCTTGGTGTACAAGTGATTATTACAGACCCTG
AAAAATTGGACCAAATTAGACAGAGAGAATCAGATATCACCAAGGAGAGAATTCAGAAGATCCTGGCAACTGGTGCCAAC
GTTATTCTGACCACTGGTGGAATTGATATGTGTCTAAAGTACTTTGTGGAGGCTGGCGCCATGGAAGTTAGAAGAGTTTT
GAAAAAGGATCTTAAGCGTATTGCTAAAACTTCTGGAGCAACTATTCTGTCAACCCTGGCCAATTTGGAAGGTGAAGAAA
CTTTTGAAGCTACAATGTTGGGACAAGCAGAAGAAGTGGTCCAGGAGAGAATTTGTGATGATGAATTAATCTTAATCAAA
AATACTAAGGCACGAACATCTGCATCGATTATTTTACGTGGGGCAAATGATTTCATGTGTGATGAGATGGAGCGCTCTTT
ACATGATGCTCTTTGTGTGGTGAAAAGAGTTTTGGAGTCGAAATCTGTCATTCCTGGTGGGGGTGCTGTAGAAGCAGCCC
TTTCCATTTACCTTTGAAAACTATGCAACCAGCATGGGCTCTCGGGAACAGCTTGCTATTGCAGAGTTTGCAAGATCTCT
TCTTGTTATTCCTAATACACTGGCAGTTAATGCTGCCCAAGACTCCATAGATCTGGTTGCAAAGTTAAGAGCTTTTCATA
ATGAGGCTCAAGTTAATCCAGAATGTAAAAATCTAAAATGGATTGGTCTTGATTTGATCAATGGTAAACCTCGAGACAAC
AAGCAAGCAGGAGTGTTTGAACCAACTGTAGTTAAAGTGAAGAGCTTGAAATTTGCAACAGAAGCAGCAATTACCATTCT
TCGGATTGATGACCTTATTAAATTACACCCAGAAAGTAAAGATGATAAGCATGGAGGTTATGAAGATGCTGTTCACTCTG
GAGCCCTTGATGAC

ORF - retro_itri_1274 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.92 %
Parental protein coverage: 77.7 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalCKEAVRYISENLIINTDELGRDCLINAAKTSMSSKIIGIDGDFFSNMVVDAVLAIKYTDIRGQPRYPINS
CKEAVRYISENLIINTDELGRDCLINAAKTSMSSKIIGIDGDFFSNMVVDAVLAIKYTDIRGQPRYPINS
RetrocopyCKEAVRYISENLIINTDELGRDCLINAAKTSMSSKIIGIDGDFFSNMVVDAVLAIKYTDIRGQPRYPINS
ParentalVNILKAHGRSQMESMLISGYALNCVVGSQGMPKRIVNAKIACLDFSLQKTKMKLGVQVIITDPEKLDQIR
VNILKAHGRSQMESMLISGYALN.VVGSQGMPKRIVNAK.ACLDFSLQKTKMKLGVQVIITDPEKLDQIR
RetrocopyVNILKAHGRSQMESMLISGYALNYVVGSQGMPKRIVNAKVACLDFSLQKTKMKLGVQVIITDPEKLDQIR
ParentalQRESDITKERIQKILATGANVILTTGGIDDMCLKYFVEAGAMAVRRVLKKDLKRIAKASGATILSTLANL
QRESDITKERIQKILATGANVILTTGGI.DMCLKYFVEAGAM.VRRVLKKDLKRIAK.SGATILSTLANL
RetrocopyQRESDITKERIQKILATGANVILTTGGI-DMCLKYFVEAGAMEVRRVLKKDLKRIAKTSGATILSTLANL
ParentalEGEETFEATMLGQAEEVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVVKRVLE
EGEETFEATMLGQAEEVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVVKRVLE
RetrocopyEGEETFEATMLGQAEEVVQERICDDELILIKNTKARTSASIILRGANDFMCDEMERSLHDALCVVKRVLE
ParentalSKSVVPGGGAVEAALSIYL-ENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSIDLVAKLRAFHNE
SKSV.PGGGAVEAALSIYL.ENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSIDLVAKLRAFHNE
RetrocopySKSVIPGGGAVEAALSIYL>ENYATSMGSREQLAIAEFARSLLVIPNTLAVNAAQDSIDLVAKLRAFHNE
ParentalAQVNPERKNLKWIGLDLINGKPRDNKQAGVFEPTIVKVKSLKFATEAAITILRIDDLIKLHPESKDDKHG
AQVNPE.KNLKWIGLDLINGKPRDNKQAGVFEPT.VKVKSLKFATEAAITILRIDDLIKLHPESKDDKHG
RetrocopyAQVNPECKNLKWIGLDLINGKPRDNKQAGVFEPTVVKVKSLKFATEAAITILRIDDLIKLHPESKDDKHG
ParentalGYEDAVHSGALDD
GYEDAVHSGALDD
RetrocopyGYEDAVHSGALDD

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_1274 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1274 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 14 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000154051 retrocopy
retro_amel_828,
Callithrix jacchus ENSCJAG000000117922 retrocopies
retro_cjac_1867, retro_cjac_2193,
Equus caballus ENSECAG000000179531 retrocopy
retro_ecab_798,
Homo sapiens ENSG000001204381 retrocopy
retro_hsap_3722,
Gorilla gorilla ENSGGOG000000140631 retrocopy
retro_ggor_2514,
Microcebus murinus ENSMICG000000079981 retrocopy
retro_mmur_795,
Macaca mulatta ENSMMUG000000128461 retrocopy
retro_mmul_1696,
Oryctolagus cuniculus ENSOCUG000000138471 retrocopy
retro_ocun_1577,
Pongo abelii ENSPPYG000000171461 retrocopy
retro_pabe_3135,
Pan troglodytes ENSPTRG000000187601 retrocopy
retro_ptro_2617,
Pteropus vampyrus ENSPVAG000000053161 retrocopy
retro_pvam_522,
Sorex araneus ENSSARG000000024631 retrocopy
retro_sara_624,
Sarcophilus harrisii ENSSHAG000000151281 retrocopy
retro_shar_830,
Ictidomys tridecemlineatus ENSSTOG00000005572 1 retrocopy
retro_itri_1274 ,


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