RetrogeneDB ID:

retro_itri_78

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393623.1:488470..489820(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000029028
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPH1
Ensembl ID:ENSSTOG00000016376
Aliases:None
Description:heterogeneous nuclear ribonucleoprotein H1 (H) [Source:HGNC Symbol;Acc:5041]


Retrocopy-Parental alignment summary:






>retro_itri_78
ATGATGCTGAGCACTGAAGGCAGGGAGGGGTTCGTGGTGAAGGTCAGGGGCCTACCCTGGTCCTGCTCAGCTGATGAAGT
GATGCGCTTCTTCTCTGATTGTAAAATCCAAAATGGCACATCAGGTATTCGTTTCATCTACACCAGAGAAGGCAGACCAA
GTGGTGAAGCATTTGTTGAACTTGAATCTGAAGATGAAGTGAAATTGGCTTTGAAGAAGGACAGAGAAACCATGGGACAT
AGATATGTTGAAGTATTCAAGTCCAACAGTGTTGAAATGGATTGGGTGTTGAAGCATACAGGTCCGAATAGTCCTGATAC
TGCCAACGATGGCTTCGTCCGGCTTAGAGGACTCCCATTTGGCTGTAGCAAGGAAGAGATTGTTCAGTTCTTTTCAGGGT
TGGAAATTGTGCCAAATGGGATGACACTGCCGGTGGACTTTCAGGGGCGGAGCACAGGGGAGGCTTTTGTGCAGTTTGCT
TCACAGGAGATAGCTGAAAAGGCCTTAAAGAAACACAAGGAAAGGATAGGGCACAGGTACATTGAAATCTTCAAGAGTAG
CAGAGCTGAAGTCCGAACCCATTATGACCCCCCTCGAAAGCTCATGGCTATGCAGCGACCAGGTCCTTACGATAGGCCAG
GAGCTGGCAGAGGATATAATAGCATTGGCAGAGGAGCTGGTTTTGAGAGGATGAGGCGGGGGGCATATGGTGGAGGGTAT
GGAGGCTATGATGACTATGGTGGCTATAACGATGGGTATGGCTTTGGGTCTGATAGATTTGGAAGAGACCTCAATTATTG
TTTCTCAGGAATGTCAGATCACAGATATGGAGATGGTGGGTCCAGTTTCCAGAGCACCACAGGGCATTGTGTACACATGA
GGGGGTTACCTTACAGAGCTACCGAGAATGATATTTACAATTTTTTCTCCCCTCTTAATCCCATGAGAGTACACATTGAA
ATTGGACCAGATGGCAGAGTTACTGGTGAGGCAGATGTTGAATTTGCTACTCATGAAGATGCTGTGGCAGCTATGGCAAA
AGATAAAGCTAATATGCAACACAGATATGTGGAGCTCTTTTTGAACTCTACTGCAGGAACAAGTGGAGGGGCTTATGATC
ACAGCTATGTAGAACTCTTTTTGAATTCTACAGCAGGGGCAAGTGGTGGTGCTTATGGTAGCCAAATGATGGGAGGGATG
GGCTTATCCAACCAGTCTAGTTATGGGGGTCCTGCCAGCCAGCAGCTGAGTGGTGGTTATGGAGGTGGTTATGGTGGTCA
GAGCAGTATGAGTGGTTATGACCAAGTTCTGCAGGAAAACTCCAGTGACTATCAGTCAAACCTTGCTTAG

ORF - retro_itri_78 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.07 %
Parental protein coverage: 94.49 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMMLGTEGGEGFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLA
MML.TEG.EGFVVKVRGLPWSCSADEV.RFFSDCKIQNG..GIRFIYTREGRPSGEAFVELESEDEVKLA
RetrocopyMMLSTEGREGFVVKVRGLPWSCSADEVMRFFSDCKIQNGTSGIRFIYTREGRPSGEAFVELESEDEVKLA
ParentalLKKDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
LKKDRETMGHRYVEVFKSN.VEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
RetrocopyLKKDRETMGHRYVEVFKSNSVEMDWVLKHTGPNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNG
ParentalITLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
.TLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
RetrocopyMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPY
ParentalDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYNGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
DRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDY.GYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
RetrocopyDRPGAGRGYNSIGRGAGFERMRRGAYGGGYGGYDDYGGYNDGYGFGSDRFGRDLNYCFSGMSDHRYGDGG
ParentalSTFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEDAVAAMSKDKA
S.FQSTTGHCVHMRGLPYRATENDIYNFFSPLNP.RVHIEIGPDGRVTGEADVEFATHEDAVAAM.KDKA
RetrocopySSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKA
ParentalNMQHRYVELFLNSTAGASGGAYEHRYVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGGY
NMQHRYVELFLNSTAG.SGGAY.H.YVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGGY
RetrocopyNMQHRYVELFLNSTAGTSGGAYDHSYVELFLNSTAGASGGAYGSQMMGGMGLSNQSSYGGPASQQLSGGY
ParentalGGGYGGQSSMSGYGSQGAMNSSYYNS
GGGYGGQSSMSGY......NSS.Y.S
RetrocopyGGGYGGQSSMSGYDQVLQENSSDYQS

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_78 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_78 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 23 parental genes, and 35 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000093891 retrocopy
retro_btau_130,
Canis familiaris ENSCAFG000000003362 retrocopies
retro_cfam_200, retro_cfam_230,
Choloepus hoffmanni ENSCHOG000000038414 retrocopies
retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Callithrix jacchus ENSCJAG000000099311 retrocopy
retro_cjac_127,
Dipodomys ordii ENSDORG000000054531 retrocopy
retro_dord_3,
Equus caballus ENSECAG000000144291 retrocopy
retro_ecab_94,
Echinops telfairi ENSETEG000000113031 retrocopy
retro_etel_50,
Gorilla gorilla ENSGGOG000000258442 retrocopies
retro_ggor_1299, retro_ggor_177,
Myotis lucifugus ENSMLUG000000166251 retrocopy
retro_mluc_124,
Macaca mulatta ENSMMUG000000108431 retrocopy
retro_mmul_2,
Monodelphis domestica ENSMODG000000094363 retrocopies
retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Mustela putorius furoENSMPUG000000006931 retrocopy
retro_mputfur_156,
Mus musculus ENSMUSG000000078501 retrocopy
retro_mmus_142,
Nomascus leucogenys ENSNLEG000000266583 retrocopies
retro_nleu_1668, retro_nleu_28, retro_nleu_48,
Ochotona princeps ENSOPRG000000035131 retrocopy
retro_opri_11,
Procavia capensis ENSPCAG000000067151 retrocopy
retro_pcap_4,
Pteropus vampyrus ENSPVAG000000076701 retrocopy
retro_pvam_23,
Sorex araneus ENSSARG000000030241 retrocopy
retro_sara_29,
Sarcophilus harrisii ENSSHAG000000182041 retrocopy
retro_shar_674,
Ictidomys tridecemlineatus ENSSTOG000000115692 retrocopies
retro_itri_1828, retro_itri_523,
Ictidomys tridecemlineatus ENSSTOG000000116761 retrocopy
retro_itri_647,
Ictidomys tridecemlineatus ENSSTOG00000016376 2 retrocopies
retro_itri_66, retro_itri_78 ,
Vicugna pacos ENSVPAG000000074852 retrocopies
retro_vpac_594, retro_vpac_614,


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