RetrogeneDB ID: | retro_cfam_221 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | AAEX03021070.1:23847..25644(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000025557 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCAFG00000002736 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cfam_221
ATGCTGCGTCAAGCACTTCGCAAGTTTGGTCAAAAGCTGGTACACAGACGTCCACTGGAACAAGATGTATATGAGTTTAA
ATATGGTGGAAGCCTGAGCACTCTGGATTTAGTGGCCCTGGGTGTGGGCCGCACAGTGGGGGTTGGTGTGTATCTCCTGC
TTTCTGAGGTGGCTAGTAGTCAAGCAGGACCAGCCACTATGATATGCTTCTTGGTGGCTGGCCTAACTTCGTTATTGGCT
GGGCTGTGCTATGCAGAGTTTAGCGCCCGGGTTCCGCATTCTGGTTCCGCATATCTCTATTGTTTTGTCACTGTAGGTGA
ACTCTGGGCATTCATCATCGGTTGGAACCTCATCCTCTCCTTTTTTATTGATGCAATCGTTGTGATCCAGGCCTGGACCT
TAATTTTTGACTACCTGATTGTAAATCAGATCTCTGAGAGCATCTCAGAGCACATTCCCCAAGTCTTAGCAGATAATCTA
GTCTACTTTACTATGGTCCTTTGGTTTTTTCTCTTAGAAATTCAAGATCTGGGTTTTCGTGGGTTCTTCAAGGTTTTCAA
ACTATTCACATTGGTGAAACTTTTGGTTCTCAGTTTTGTCATCATCTCTGGCTTCGTTAAGGGGGACCTGCACAACTGGA
GGCTCACAGAAGAGGACTATATAAAGGCTGGACTCAATGACACCTCTAGCTTGGGCCTTCTGGGCTCTGGAGGATTCATG
CCTTTTGGCTTCCAGGGGATTCTTCATGGAGCAGCTACCTGTTTCTATGCTTTTATAGGTTTCGCCGTTATTGTTACCAG
AGTCAAAGAGTTGCACAAGCCTGAGCGTTCCATCCCCATGGGCATTGTTATTTCACTGCTCACCTGCATCTTGGTGTATT
TAGGTGTCTCTGCGGCAATTACACTTATGGTGCCTTACTACCAGCTCCGACCTGGGAGCCTCTTGCCTGAGGCATTTCTC
CATATTGGCTGGGGCCTGGCCTACTATGTTGTAGCTGTTGCAATTTTCTGTACTATTTTTGTCAGCATGTATTGGAGCTT
TACGTACCCCATACGTATTGTGATATCCATGATGGCAGACGATGGCCTCCTGTTCCCTGTGCTTGCCAGGGTCATCACTG
GCACATACGCTCAGTTAGTGTTCAGGTTATTCATTTATGTTATTGCAGTAATCATATTATTATTCTTTGGATTTGCTGAT
CTCTTGGACCTCAGGTCAATTGCGACCCTGCTATCTTATTCCCTGGTAGCTTTTTGTGTTCTCATCATCAGGTATCAGCC
TGAGAGGAGGAATATAGAAAACGAAGCAGAGGAGGAAGAGGAGAATGAGGGAAATGAAGTAGAGGTGCAAGAGGAGAACC
CACCTGCAGCAGAGAAGCTAACTCTACAGGGACTACTTTTTCCAGGCAGCTTCACCCCCACTCCACTCTCTGGCCGGGTT
GTCTATGTTTGCTCCTCACTGCTTGTTCTGCTGCTGATTGTTCTTTGCCTGGTGCTGGCCCAGTGGCCAGGTCTGCTTTC
TGGAGACCCAGGGTGGATCACAGTAGTTGTGTTGCTCCTGGTGGTCATCACTGGGATCACTGGGATCATCTGGAGACAGC
CACAGAGCTCCCATCTGCCTCATTTTAAGGTACCTGGTCTGCCTCTCCTCCCACTCCTGAGCATCTTTCTGAATGTTTGC
CTTATGATGCAGATGACCGCTGGCACTTGGGTCCGATTTGGTGCCTGGATGTTGACTGGGTTTATTATCTACTTCGCCTA
TGGGATCCAGCACAGCCTTAAGGACCAAAACCATAGA
ORF - retro_cfam_221 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.22 % |
| Parental protein coverage: | 96.18 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MLCQHVCQFGQKLLRRRPLGPKQGAESHLARCLNTLDLVALGVGSTLGAGVYILAGEVAKDKAGPAIIIC |
| ML.Q....FGQKL..RRPL......E......L.TLDLVALGVG.T.G.GVY.L..EVA...AGPA..IC | |
| Retrocopy | MLRQALRKFGQKLVHRRPL-EQDVYEFKYGGSLSTLDLVALGVGRTVGVGVYLLLSEVASSQAGPATMIC |
| Parental | FLVAALSSVLSGLCYAEFGARVPGSGSAYLYSYVTVGQLCAFITGWNLILSYVIGAASVARAWSSAFDDL |
| FLVA.L.S.L.GLCYAEF.ARVP.SGSAYLY..VTVG.L.AFI.GWNLILS..I.A..V..AW...FD.L | |
| Retrocopy | FLVAGLTSLLAGLCYAEFSARVPHSGSAYLYCFVTVGELWAFIIGWNLILSFFIDAIVVIQAWTLIFDYL |
| Parental | TGNQVSRVLQGSFSLQAPHVLATHLDFFALGLVLLLTGLLVLGASESALVTKIFTGVNVLVLSFIILSGF |
| ..NQ.S.....S.S...P.VLA..L..F...L...L.....LG......V.K.FT.V..LVLSF.I.SGF | |
| Retrocopy | IVNQISE----SISEHIPQVLADNLVYFTMVLWFFLLEIQDLGFRGFFKVFKLFTLVKLLVLSFVIISGF |
| Parental | IKGDLHHWQLTEEDYKLAMSASNDTSSLGPLGSGGFMPFGFEGILHGAATCFYAFIGFDCIATTGEEARD |
| .KGDLH.W.LTEEDY..A....NDTSSLG.LGSGGFMPFGF.GILHGAATCFYAFIGF..I.T...E... | |
| Retrocopy | VKGDLHNWRLTEEDYIKA--GLNDTSSLGLLGSGGFMPFGFQGILHGAATCFYAFIGFAVIVTRVKELHK |
| Parental | PQRSIPLSIIISLFICFLAYFGVSAALTLMMPYYQIHPGSPLPQAFLYVGWAPARYTVAAGTLCALSSSL |
| P.RSIP..I.ISL..C.L.Y.GVSAA.TLM.PYYQ..PGS.LP.AFL..GW..A.Y.VA....C....S. | |
| Retrocopy | PERSIPMGIVISLLTCILVYLGVSAAITLMVPYYQLRPGSLLPEAFLHIGWGLAYYVVAVAIFCTIFVSM |
| Parental | LGTM-FPMPRVIYAMADDGLLFRGLARIHPCTHTPMMATIVSGTFAAFMAFLFELSDLVDLMSIGTLLAY |
| ......P...VI..MADDGLLF..LAR....T.............A......F...DL.DL.SI.TLL.Y | |
| Retrocopy | YWSFTYPIRIVISMMADDGLLFPVLARVITGTYAQLVFRLFIYVIAVIILLFFGFADLLDLRSIATLLSY |
| Parental | SLVVFSVLVLRYQPDQNLSKNEKTEMEIIERKPAPQASSLKSVPEAGTVQALWSLCNPVNTTPTLKSGHI |
| SLV.F.VL..RYQP......NE..E.E..E..............E..T.Q.L........T......... | |
| Retrocopy | SLVAFCVLIIRYQPERRNIENEAEEEEENEGNEVEVQEENPPAAEKLTLQGLLFPGSFTPTPLSGRVVYV |
| Parental | AYGCALLLALLLTILCLILAQWPSHLFSGDPVYITGCVLLLLLIIGLTFIIWRQPQNPTPFHFKVPALPV |
| ......LL...L......LAQWP..L.SGDP..IT..VLLL..I.G.T.IIWRQPQ.....HFKVP.LP. | |
| Retrocopy | CSSLLVLLLIVLCL---VLAQWPG-LLSGDPGWITVVVLLLVVITGITGIIWRQPQSSHLPHFKVPGLPL |
| Parental | LPLVSIFTNVYLMMQMTSGTWARFGVWMVIGFAIYFGYGIRHSLE |
| LPL.SIF.NV.LMMQMT.GTW.RFG.WM..GF.IYF.YGI.HSL. | |
| Retrocopy | LPLLSIFLNVCLMMQMTAGTWVRFGAWMLTGFIIYFAYGIQHSLK |
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 |
|---|---|---|
| SRP012049_cerebellum | 0 .00 RPM | 0 .17 RPM |
| SRP017611_brain | 0 .00 RPM | 0 .24 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .00 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_221 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_221 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_221 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000002736 | 2 retrocopies |
retro_cfam_131, retro_cfam_221 ,
|
| Canis familiaris | ENSCAFG00000016908 | 2 retrocopies |