RetrogeneDB ID: | retro_mmus_1841 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 19:60080077..60081586(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Csf3r | ||
| Ensembl ID: | ENSMUSG00000028859 | ||
| Aliases: | Csf3r, Cd114, Csfgr, G-CSF-R, G-CSFR | ||
| Description: | colony stimulating factor 3 receptor (granulocyte) [Source:MGI Symbol;Acc:MGI:1339755] |
Retrocopy-Parental alignment summary:
>retro_mmus_1841
GCCCCCACCATCAGACTGGACACGTGATGTCAGAAGAAGCAACTGGATCCAGGGATAGTGAGTGTGCAGCTGTTCTGGAA
GCCAACGCCCCTGCAGGAAGACAGTGGACAGATCCAGGGCTACCTGCTGTCCTGGAGTTCCTCAGATCACCAAGGGCAGG
ACATACACCTTTGCAACACCACACAGCTCAGCTGTATCTTCCTCCTGCCCTCAGAGGCCCAGAACGTGACCCTTGTGGCC
TACAACAAAGCAGGGACCTCTTCACCTACTACAGTGGTTTTCCTGGAGAACAAAGGTCCAGCTGTGACCGGACTCCATGC
CATGGCCCAAGACCTTAACACCATCTGGGTAGACTGAGCCCCCAGCCTTCTGCCTCAGGGCTATCTCATTGAGTGGGAAA
TGAGTTCTCCCAGCTACAATAACAGCTATAAGTCCTGGATGATAGAACCTAATGGGAACATCACTGGAATTCTGTTAAAG
GACAACATAAATCCCTTTCAGCTCTACAGAATCACAGTGGCTCCCCTATACCCAGGCATCGTGGGACCCCCTATAAATGT
CTACACCTACACTGGAGAGAGAGCTCTTCCTCATGCTCCAGCGCTACATCTAAAGCATGTTGGCACAACCTGGGGACAGC
TGGAGTGGGTACCTGAGGCCCCTAGGCTAGGGATGATACCCCTCACCCACTACACCATCTTCTGGGCCTATGCTGGGGAC
CACTCCTTCTCCTTCACCCTGAACATCTCCCTCCATGACTTTGTCCTGAAGCACCTGGAGCCTGCCAGTTTGTATCATGT
CTACCTCATGGCCACCAGTCGAGCAGGGTCCACCAACAGTACAGGCCTTACCCTGAGGACCCTAGATCCATCTGACATAA
ACATTTTCCTGGGCATACTTTGCTTAGTATTCTTGTCCATTACCCGTGTAATCACCTGGCTCTGCTACAAGCACAGAGGA
AAGATTTTCTTCTGGTCAGATGTGCCAGACCCAGCCCACAGTAGTCTGAGCTCCTGGTTGCCCACCATCATGACAGAGGA
AACCTTCCAGTTACCCACCTTCTGGGACTCCAGCTTGCCATCAATCACCAAGATCACTGAACTGGAGGAAGACAAGAAAC
CGACCCACTGGGATTCTGAAAGTTCTGGGAATGGTAGCCTTCCAGCCCTGGTTCAGGCCTATGTGCTCCAAGGAGATCCA
ACAGAAATTTCCAACCAGTCCCAGCCTCCCTCTCGCACTGGTGACCAGGTCCTCTATGGTCAGGTGCTTGAGAGCCCCAC
CAGCCCAGGAGTAATGCAGTACATTCACTCTAACTCCACTCAGCCCCTCTTGGGAGGCCTCACCCCTAGCCCTACATCTT
ATGAAAACATCTGGTTCCATTCAAGACCCCAGGAGACCTTTGTGCCCCAACCTCCAAGCCAGGAAGATGACTGTGTCTTT
GGGCCTCCATTTGATTTTTCCCTCTTTCAGGGGCTCCAGGTCCATGGAGTTGAAGAACAAGGGGGTTTC
ORF - retro_mmus_1841 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.85 % |
| Parental protein coverage: | 60.22 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | APTIRLDTWCQKKQLDPGTVSVQLFWKPTPLQEDSGQIQGYLLSWSSPDHQGQDIHLCNTTQLSCIFLLP |
| APTIRLDT.CQKKQLDPG.VSVQLFWKPTPLQEDSGQIQGYLLSWSS.DHQGQDIHLCNTTQLSCIFLLP | |
| Retrocopy | APTIRLDT*CQKKQLDPGIVSVQLFWKPTPLQEDSGQIQGYLLSWSSSDHQGQDIHLCNTTQLSCIFLLP |
| Parental | SEAQNVTLVAYNKAGTSSPTTVVFLENEGPAVTGLHAMAQDLNTIWVDWEAPSLLPQGYLIEWEMSSPSY |
| SEAQNVTLVAYNKAGTSSPTTVVFLEN.GPAVTGLHAMAQDLNTIWVD..APSLLPQGYLIEWEMSSPSY | |
| Retrocopy | SEAQNVTLVAYNKAGTSSPTTVVFLENKGPAVTGLHAMAQDLNTIWVD*-APSLLPQGYLIEWEMSSPSY |
| Parental | NNSYKSWMIEPNGNITGILLKDNINPFQLYRITVAPLYPGIVGPPVNVYTFAGERAPPHAPALHLKHVGT |
| NNSYKSWMIEPNGNITGILLKDNINPFQLYRITVAPLYPGIVGPP.NVYT..GERA.PHAPALHLKHVGT | |
| Retrocopy | NNSYKSWMIEPNGNITGILLKDNINPFQLYRITVAPLYPGIVGPPINVYTYTGERALPHAPALHLKHVGT |
| Parental | TWAQLEWVPEAPRLGMIPLTHYTIFWADAGDHSFSVTLNISLHDFVLKHLEPASLYHVYLMATSRAGSTN |
| TW.QLEWVPEAPRLGMIPLTHYTIFWA.AGDHSFS.TLNISLHDFVLKHLEPASLYHVYLMATSRAGSTN | |
| Retrocopy | TWGQLEWVPEAPRLGMIPLTHYTIFWAYAGDHSFSFTLNISLHDFVLKHLEPASLYHVYLMATSRAGSTN |
| Parental | STGLTLRTLDPSDLNIFLGILCLVLLSTTCVVTWLCCKRRGKTSFWSDVPDPAHSSLSSWLPTIMTEETF |
| STGLTLRTLDPSD.NIFLGILCLV.LS.T.V.TWLC.K.RGK..FWSDVPDPAHSSLSSWLPTIMTEETF | |
| Retrocopy | STGLTLRTLDPSDINIFLGILCLVFLSITRVITWLCYKHRGKIFFWSDVPDPAHSSLSSWLPTIMTEETF |
| Parental | QLPSFWDSSVPSITKITELEEDKKPTHWDSESSGNGSLPALVQAYVLQGDPREISNQSQPPSRTGDQVLY |
| QLP.FWDSS.PSITKITELEEDKKPTHWDSESSGNGSLPALVQAYVLQGDP.EISNQSQPPSRTGDQVLY | |
| Retrocopy | QLPTFWDSSLPSITKITELEEDKKPTHWDSESSGNGSLPALVQAYVLQGDPTEISNQSQPPSRTGDQVLY |
| Parental | GQVLESPTSPGVMQYIRSDSTQPLLGGPTPSPKSYENIWFHSRPQETFVPQPPNQEDDCVFGPPFDFPLF |
| GQVLESPTSPGVMQYI.S.STQPLLGG.TPSP.SYENIWFHSRPQETFVPQPP.QEDDCVFGPPFDF.LF | |
| Retrocopy | GQVLESPTSPGVMQYIHSNSTQPLLGGLTPSPTSYENIWFHSRPQETFVPQPPSQEDDCVFGPPFDFSLF |
| Parental | QGLQVHGVEEQGGF |
| QGLQVHGVEEQGGF | |
| Retrocopy | QGLQVHGVEEQGGF |
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 |
|---|---|---|
| SRP007412_brain | 0 .02 RPM | 5 .89 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 3 .82 RPM |
| SRP007412_heart | 0 .00 RPM | 1 .34 RPM |
| SRP007412_kidney | 0 .00 RPM | 4 .47 RPM |
| SRP007412_liver | 0 .00 RPM | 2 .81 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .87 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1841 was not detected
No EST(s) were mapped for retro_mmus_1841 retrocopy.
No TSS is located nearby retro_mmus_1841 retrocopy 5' end.
retro_mmus_1841 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1841 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000028859 | 1 retrocopy |
retro_mmus_1841 ,
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