RetrogeneDB ID:

retro_cjac_3036

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:7:147624312..147625291(-)
Located in intron of:ENSCJAG00000013392
Retrocopy
information
Ensembl ID:ENSCJAG00000034390
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KRT18
Ensembl ID:ENSCJAG00000018165
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3036
CGGTTCCTGGAGAGCAAAATCTGGGAGTACCTAAAGAAGAAGGGACCCCAGCTCAGAAACTGGGGCCATTACTTCAAAAC
CATCAAGGACCTGAGGGATCAGACATTCATAAATACTGTGGACAACGCCTGCATCATTCTGCAAATCAACAATGCCCGTC
TTGCCGCTGATGACTTTAGAGTCAAGTATGCAACAGAGCTGGCCATGTCCCAGTCTATGGAGAGTGACCTCCATGGACTC
TGAAAGGTCACTGATGACACCAATATCATTTGGCTGCAGCTGGAAACAGAGATCGATGCTCTCAAGGAGGAGCTGTTCTT
CATGCAGAAGAAGCACAATGGGGAAGTAAAAAGCCTACAAGCCCCAAGTACCAGCTCTGGGTTGACTGTGGAGGTAAATG
CTCCCAAATCTCAGGACCTGTCCAAGATGATGGCCAGACATCCAGGCCTAAGACAATGAGCTAGCTTGGAAGAACCGACA
GGAGCTAGACAAGTACTGGCCTCAGCAGATTGAAGAGGACATGATAGTGGTCGCCATGCAGTCTGCTGAGGTTGGAGCTG
CTGAGATGATGCTCATGGAGCTAAGACGTACAATGCAGTCCTTAAAGATCGACCTGGACTCAATAAGAAATCTGAAGGCC
AGCTTACAGAACAGCCTGAGGGAAGTGGAGGCCCGCTACTCCCTGCAGATGGAGCAGCTCAACGGGATCCTGCTGCACCT
GGAAGAGCCAGAACTGGCACAGACCTGGGCAGAGAAGCAGTGCCAGGCCAAGCAGTACAAGGTCCTGTTGAACATCAAGG
TCAAGCTGGAGGCTGAGATCGCCACCTACCACCGCCTGTTGGAAGATGGCGAGGACTTTAATCTTAGCGATGCCCTGGAC
AGCAGCAACTCCATCTAAACCATCCAAAAGACCACCACCTGCTGGATAGTGGATGGCAAAGTGATATCTGAGACCAATGA
TACCAAAGTTCTGAGACAT

ORF - retro_cjac_3036 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.39 %
Parental protein coverage: 75.64 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRKLEIKIREHLEKKGPQVRDWGHYFKTIEDLRAQIFSNTVDNARIVLQIDNARLAADDFRVKYETELAMR
R.LE.KI.E.L.KKGPQ.R.WGHYFKTI.DLR.Q.F.NTVDNA.I.LQI.NARLAADDFRVKY.TELAM.
RetrocopyRFLESKIWEYLKKKGPQLRNWGHYFKTIKDLRDQTFINTVDNACIILQINNARLAADDFRVKYATELAMS
ParentalQSVESDIHGLRKVIDDTNVTRLQLETEIEALKEELLFMKKNHEEEVNGLQAQIASSGLTVEVDTPKSQDL
QS.ESD.HGL.KV.DDTN...LQLETEI.ALKEEL.FM.K.H..EV..LQA...SSGLTVEV..PKSQDL
RetrocopyQSMESDLHGL*KVTDDTNIIWLQLETEIDALKEELFFMQKKHNGEVKSLQAPSTSSGLTVEVNAPKSQDL
ParentalAKIMA-EIRAQYDELARKNREELDKYWTQQIEESTTIVTTQSTEVETAGMTLTELRRTVQSLEIDLDSMR
.K.MA..I.A...ELA.KNR.ELDKYW.QQIEE....V..QS.EV..A.M.L.ELRRT.QSL.IDLDS.R
RetrocopySKMMA>DIQA*DNELAWKNRQELDKYWPQQIEEDMIVVAMQSAEVGAAEMMLMELRRTMQSLKIDLDSIR
ParentalNQKISLENSLREVEARYALQMEQLNGILLHLES-ELAQTRAEGQRQAQEYEALLNIKVKLEAEIATYRRL
N.K.SL.NSLREVEARY.LQMEQLNGILLHLE..ELAQT.AE.Q.QA..Y..LLNIKVKLEAEIATY.RL
RetrocopyNLKASLQNSLREVEARYSLQMEQLNGILLHLEEPELAQTWAEKQCQAKQYKVLLNIKVKLEAEIATYHRL
ParentalLEDGEDFSLSDALNSSSNSMQTIQKTTTRRIVDGKVVSETNDTKVLRH
LEDGEDF.LSDAL..SSNS..TIQKTTT..IVDGKV.SETNDTKVLRH
RetrocopyLEDGEDFNLSDALD-SSNSI*TIQKTTTCWIVDGKVISETNDTKVLRH

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






(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
SRP051959_colon 1 .71 RPM 101 .02 RPM
SRP051959_heart 1 .63 RPM 1 .18 RPM
SRP051959_kidney 0 .87 RPM 16 .24 RPM
SRP051959_liver 0 .87 RPM 37 .95 RPM
SRP051959_lung 2 .31 RPM 14 .41 RPM
SRP051959_lymph_node 4 .31 RPM 0 .66 RPM
SRP051959_skeletal_muscle 1 .16 RPM 0 .04 RPM
SRP051959_spleen 1 .95 RPM 1 .24 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3036 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3036 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3036 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_434
Pan troglodytes retro_ptro_193
Pongo abelii retro_pabe_290

Parental genes homology:
Parental genes homology involve 21 parental genes, and 338 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000119812 retrocopies
Canis familiaris ENSCAFG0000000715410 retrocopies
Callithrix jacchus ENSCJAG00000018165 29 retrocopies
Cavia porcellus ENSCPOG000000026181 retrocopy
Echinops telfairi ENSETEG000000081301 retrocopy
Homo sapiens ENSG0000011105760 retrocopies
Gorilla gorilla ENSGGOG0000001015728 retrocopies
Macropus eugenii ENSMEUG0000001226214 retrocopies
Myotis lucifugus ENSMLUG000000224398 retrocopies
Macaca mulatta ENSMMUG000000319114 retrocopies
Mustela putorius furoENSMPUG000000063692 retrocopies
Mus musculus ENSMUSG000000230432 retrocopies
Nomascus leucogenys ENSNLEG0000001773245 retrocopies
Oryctolagus cuniculus ENSOCUG000000276911 retrocopy
Pongo abelii ENSPPYG0000000456360 retrocopies
Pan troglodytes ENSPTRG0000000499658 retrocopies
Pteropus vampyrus ENSPVAG000000093612 retrocopies
Rattus norvegicus ENSRNOG000000473933 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000155873 retrocopies
Tursiops truncatus ENSTTRG000000129772 retrocopies
Vicugna pacos ENSVPAG000000074213 retrocopies



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