RetrogeneDB ID:

retro_itri_73

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393582.1:103303..104524(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000021765
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:NKAP
Ensembl ID:ENSSTOG00000001134
Aliases:None
Description:NFKB activating protein [Source:HGNC Symbol;Acc:29873]


Retrocopy-Parental alignment summary:






>retro_itri_73
ATGGCTCCAGTATCTCGGTCCAGCTATTCCGAGGACCCCCCAGGTTCTCAGAGGCCACGACGCAGCTCTTCTGGGAGCCC
ACCGTCTGCACGGAACAGGCGCTCCCCTTGGGGTGGCAGTTCCCGCCCTCACTCCCGAGGACCAGAGGGCCTCAAGCCTC
CCTGGGTTGGGGTGAGCGTTGGCCCTTCTTATCCCCTTAGCCGCGCTGAGTCTCGGGAGCGGCCTCCAGGCCTCCACAGC
TACGACTTCTCGTCCTCCTCTTCAATTTACTGTGGGGGATATCGCCACCACCACCGTCACCACCACTACGGGGGCGATTG
GCAGTGGGCAGAACACTATGAGAAGGAAAAGGAGGAGAGCTATCGGCAAAGGAGGCTGAAGGAGAGAGAGAGAATTGGGG
AGTTGGGTGCGCCTGAAGTGTGGGGGCTGTCACCAAAGTTTCCTGAGCCAGATTCTGATGAACATACCCCAGTTGAAGAG
GAGCTGAAGAATCAAAAGAGTACCAATTCAGATTCCAGCTCTGAAGAAAAAAGAAAAAAGAAGACCAGTCGTTCAAAAAA
GAAAAAAAGAAAGAAGAAGTCCTCCAAAAGAAAACATAGGAAGTATTCTGATAATGATAGTAATTCAGTCTCTGACACTG
ATTCTAGCTCCGATGATGATAAAAAGAAAGTCAAAAAACCTAAGAAGAAAGACAAGAAAAAGAAACACAGAGCGAAAAAA
TACAAGAAAAAGAATAAGAAGACTAAAAAAGAATCTAGTGACACAAGCTATAAAGCTTCAGAAGGGGAATTTCCAGAAGG
TATCTGGATGGGACAGTCAAAGACTGCAGATACAATGGATTTAATAGGCCCAGAAGCACCTATAATACATACCACTCAAG
ATGAGAAACCTTTGAACTATGGTCATGCTCTGCTCCCAGGTGAAGGTGCAGCTATGGCTGAGTATGTAAAAGCTGGAAAG
CGTATCCCGCGAAGAGGTGAAATTGGGTTGACAAGTGAAGAGATTGCCTCATTTGAATGCTCGGGTTATGTCATGAGTGG
TAGCAGACATCGCAGAATGGAGGCTGTAAGACTGCGTAAAGAGAATCAAATTTACAGTGCTGATGAAAAGAGAGCTCTTG
CATCCTTTAACCAAGAAGAGAGAAGAAAGAGAGAGAATAAGATTCTAGCCAGTTTCCGAGAGATGGTGTACAGAAAGACA
AAAGGGAAAGATGACAAGTAA

ORF - retro_itri_73 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.48 %
Parental protein coverage: 74.34 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalYGSDKPWPSLLDKEREESLRQKRLSERERIGELGAPEVWGLSPKNPEPDSDEHTPVEDEEPKKSTTSASS
YG.D..W.....KE.EES.RQ.RL.ERERIGELGAPEVWGLSPK.PEPDSDEHTPVE.E......T...S
RetrocopyYGGDWQWAEHYEKEKEESYRQRRLKERERIGELGAPEVWGLSPKFPEPDSDEHTPVEEELKNQKSTNSDS
ParentalSEDEKKKKKKSSHSKEKSKKKRKKKSSKRKHKKYSEDSDSDSDSETDSSDEVTKRRAKKNKKKEKKKKHR
S..EK.KKK.S.......KKKRKKKSSKRKH.KYS.D.DS.S.S.TDSS....K...KK.KKK.KKKKHR
RetrocopySSEEKRKKKTS----RSKKKKRKKKSSKRKHRKYS-DNDSNSVSDTDSSSDDDKKKVKKPKKKDKKKKHR
ParentalSKKYKKKKSKKNRKESSDSSSKDSQEEFLENPWKDRSKAEEPSDLIGPEAPKTLASQDDKPLNYGHALLP
.KKYKKK..KK..KESSD.S.K.S..EF.E..W...SK.....DLIGPEAP.....QD.KPLNYGHALLP
RetrocopyAKKYKKK-NKKTKKESSDTSYKASEGEFPEGIWMGQSKTADTMDLIGPEAPIIHTTQDEKPLNYGHALLP
ParentalGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASF
GEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASF
RetrocopyGEGAAMAEYVKAGKRIPRRGEIGLTSEEIASFECSGYVMSGSRHRRMEAVRLRKENQIYSADEKRALASF
ParentalNQEERRKRENKILASFREMVYRKTKGKDDK
NQEERRKRENKILASFREMVYRKTKGKDDK
RetrocopyNQEERRKRENKILASFREMVYRKTKGKDDK

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_73 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_73 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 15 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000184331 retrocopy
retro_cfam_172,
Dasypus novemcinctus ENSDNOG000000000721 retrocopy
retro_dnov_50,
Echinops telfairi ENSETEG000000010071 retrocopy
retro_etel_1882,
Felis catus ENSFCAG000000043921 retrocopy
retro_fcat_10,
Homo sapiens ENSG000001018821 retrocopy
retro_hsap_15,
Loxodonta africana ENSLAFG000000029621 retrocopy
retro_lafr_37,
Macaca mulatta ENSMMUG000000123821 retrocopy
retro_mmul_121,
Mus musculus ENSMUSG000000164091 retrocopy
retro_mmus_279,
Nomascus leucogenys ENSNLEG000000149221 retrocopy
retro_nleu_88,
Otolemur garnettii ENSOGAG000000010041 retrocopy
retro_ogar_239,
Pongo abelii ENSPPYG000000206791 retrocopy
retro_pabe_198,
Pan troglodytes ENSPTRG000000222331 retrocopy
retro_ptro_117,
Rattus norvegicus ENSRNOG000000311691 retrocopy
retro_rnor_93,
Sus scrofa ENSSSCG000000126131 retrocopy
retro_sscr_13,
Ictidomys tridecemlineatus ENSSTOG00000001134 1 retrocopy
retro_itri_73 ,


Copyright © RetrogeneDB 2014-2017