RetrogeneDB ID:

retro_mmus_18

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:18:43476954..43477746(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000043424
Aliases:Eif3j2, ENSMUSG00000043424, Eif3j-2, Gm9781, eIF3 p35, eIF3j-B
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Eif3j1
Ensembl ID:ENSMUSG00000027236
Aliases:None
Description:eukaryotic translation initiation factor 3, subunit J1 [Source:MGI Symbol;Acc:MGI:1925905]


Retrocopy-Parental alignment summary:






>retro_mmus_18
ATGGCGGCGGCGGCGGCGGCGGCGGCGGCAGCGGCGGCGGGGGACTCAGACTCTTGGGACGCGGACACGTTCTCTATGGA
GGACCCGGTGCGGAAGGTCGCGGGCGGCGGCACGGCCGGCGGGGACCGCTGGGAAGGCGAGGACGAGGACGAGGACGTGA
AGGATAACTGGGATGATGATGATGATGAAAATAAAGAGGAAGCAGAAGTCAAACCAGAAGTAAAAATTTCAGAGAAGAAA
AAAATAGCAGAAAAGATAAAAGAGAAAGAACGGCAGCAGAAGAAAAGGCAAGAAGAAATTAAAAAGAGGTTAGAAGAACC
TGAAGAATCTAAAGTACTAACACCTGAAGAGCAATTAGCAGATAAACTCCGGCTAAAGAAATTACAGGAAGAGTCAGACC
TTGAATTAGCAAAAGAAACTTTTGGTGTTAATAATACCGTTTATGGAATAGATGCTATGAACCCATCTTCAAGAGATGAC
TTCACAGAGTTTGGAAAGTTACTAAAAGATAAAATTACACAATATGAAAAATCACTATATTATGCCAGTTTTTTGGAAGC
CTTAGTTCGGGATGTCTGTATTTCATTGGAAATTGATGACTTGAAAAAGATTACCAACTCATTGACTGTGCTCTGCAGTG
AAAAACAGAAGCAAGAAAAGCAAAGCAAAGCCAAAAAGAAGAAGAAAGGCGTGGTTCCTGGAGGGGGATTAAAGGCCACC
ATGAAAGACGACCTGGCAGATTATGGTGGATATGAAGGAGGCTATGTACAAGACTATGAAGACTTCATGTGA

ORF - retro_mmus_18 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 100.0 %
Parental protein coverage: 99.62 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalAAAAAAAAAAGDSDSWDADTFSMEDPVRKVAGGGTAGGDRWEGEDEDEDVKDNWDDDDDENKEEAEVKPE
AAAAAAAAAAGDSDSWDADTFSMEDPVRKVAGGGTAGGDRWEGEDEDEDVKDNWDDDDDENKEEAEVKPE
RetrocopyAAAAAAAAAAGDSDSWDADTFSMEDPVRKVAGGGTAGGDRWEGEDEDEDVKDNWDDDDDENKEEAEVKPE
ParentalVKISEKKKIAEKIKEKERQQKKRQEEIKKRLEEPEESKVLTPEEQLADKLRLKKLQEESDLELAKETFGV
VKISEKKKIAEKIKEKERQQKKRQEEIKKRLEEPEESKVLTPEEQLADKLRLKKLQEESDLELAKETFGV
RetrocopyVKISEKKKIAEKIKEKERQQKKRQEEIKKRLEEPEESKVLTPEEQLADKLRLKKLQEESDLELAKETFGV
ParentalNNTVYGIDAMNPSSRDDFTEFGKLLKDKITQYEKSLYYASFLEALVRDVCISLEIDDLKKITNSLTVLCS
NNTVYGIDAMNPSSRDDFTEFGKLLKDKITQYEKSLYYASFLEALVRDVCISLEIDDLKKITNSLTVLCS
RetrocopyNNTVYGIDAMNPSSRDDFTEFGKLLKDKITQYEKSLYYASFLEALVRDVCISLEIDDLKKITNSLTVLCS
ParentalEKQKQEKQSKAKKKKKGVVPGGGLKATMKDDLADYGGYEGGYVQDYEDFM
EKQKQEKQSKAKKKKKGVVPGGGLKATMKDDLADYGGYEGGYVQDYEDFM
RetrocopyEKQKQEKQSKAKKKKKGVVPGGGLKATMKDDLADYGGYEGGYVQDYEDFM

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






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .09 RPM 10 .54 RPM
SRP007412_cerebellum 0 .17 RPM 7 .43 RPM
SRP007412_heart 0 .22 RPM 15 .94 RPM
SRP007412_kidney 0 .19 RPM 10 .01 RPM
SRP007412_liver 0 .33 RPM 14 .12 RPM
SRP007412_testis 0 .27 RPM 16 .10 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity may be related with retro_mmus_18 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001XVA POLR2A 18:43477717..43477798
ENCFF001YKA POLR2A 18:43477584..43477967

EST - click to see more details

No EST(s) were mapped for retro_mmus_18 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_59418324 libraries 259 libraries 203 libraries 169 libraries 117 libraries

The graphical summary, for retro_mmus_18 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_18 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_18 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000024121 retrocopy
retro_cjac_589,
Cavia porcellus ENSCPOG000000123963 retrocopies
retro_cpor_1357, retro_cpor_1358, retro_cpor_500,
Dipodomys ordii ENSDORG000000083397 retrocopies
retro_dord_208, retro_dord_364, retro_dord_451, retro_dord_470, retro_dord_633, retro_dord_738, retro_dord_746,
Equus caballus ENSECAG000000087161 retrocopy
retro_ecab_635,
Echinops telfairi ENSETEG000000050521 retrocopy
retro_etel_1376,
Homo sapiens ENSG000001041311 retrocopy
retro_hsap_4189,
Gorilla gorilla ENSGGOG000000005482 retrocopies
retro_ggor_1687, retro_ggor_41,
Macropus eugenii ENSMEUG000000103721 retrocopy
retro_meug_256,
Microcebus murinus ENSMICG000000050061 retrocopy
retro_mmur_100,
Monodelphis domestica ENSMODG000000176961 retrocopy
retro_mdom_141,
Mus musculus ENSMUSG00000027236 1 retrocopy
retro_mmus_18 ,
Nomascus leucogenys ENSNLEG000000055681 retrocopy
retro_nleu_2848,
Oryctolagus cuniculus ENSOCUG000000053761 retrocopy
retro_ocun_1350,
Otolemur garnettii ENSOGAG000000046941 retrocopy
retro_ogar_1227,
Pongo abelii ENSPPYG000000064311 retrocopy
retro_pabe_3429,


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