RetrogeneDB ID: | retro_ptro_1833 | ||
Retrocopy location | Organism: | Chimpanzee (Pan troglodytes) | |
| Coordinates: | 3:146026392..146027606(+) | ||
| Located in intron of: | ENSPTRG00000015483 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | EIF2AK1 | ||
| Ensembl ID: | ENSPTRG00000018904 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ptro_1833
GGCTGCGCTGCAGCCCGCGAGCACAAAGAGGAGGGCCACGGGGTGGAGACTGTTGCTGTGCCATCTGCCATCGACTTTTC
CACCAAGAGCCTGGACTCCAAATATGACTTATGTTCCAGCAGAACTCCAGGTATTAAAATAACCCCTACAACAGCCAACT
TTCCCTTTTGCAGTTGCAAACCAGCTGCCGCTTATTTCTTTGGTGAAGCACTTGAGCCATGTGCGTGAACCAAACCCAGT
TCATTCAAGACAGGTGTTTAAGTTACTTTGCCAGACCTTTACAAAATGGGGCTGCTGTCTTCTTTCACTTGTGACAAGTT
TAGCTCATTGAGACTACATCACCACAGAGCTATTACTCACTTAATGAGGTCCACTAAAGAGAGAGTTCATCAGGATCCTT
GTGAGGCTATTTCTCATATCCAGAAAATCAGATCAAGGGAAGTACCCTTTGAAGCACAAACTTCACGTTACTTAAATGAA
TTTGAAGAACTTGCCATCTTAGGAAAAGGTGGATATGGAAGAGTATACAAGGTCAGGAATAAATTAGATGGTCAGTATTA
TGCAATTTAAAAAATCCTGATTAAGGGTGCAACAAAAACACATTACATGAAGGAACTACGGGGAATGAAGGTGCTGGCAG
GTCTTCAGCACCCTAATATTATTCGTTATCACACTGCGTGGACAGAACATGTTCAAGTGGTCCAACCACAAGCAGACAGA
GCTTCCATTCAGTTGCCATTTCTGGAAGTGTTCTCCGACCAAGCAGACAGATACCAATACGGTGTTAAAAATGGTGAAAA
TAGCAGCTCACCCATTATCTTCGCTGAGCTCACCTCAGAAAAGAAAAACCCTTTGCAGAATCTGACACTCAAAATCAGAA
TAACAAGCTGTGAACTACACCATCAATTCCGTCTTAAGAGACACCAGTGAATTTGAATCATCCCTGGAGCTCCAGGAAAA
TGGCCTGGCTGGTTTGTCTACCTGGTCAATTGTGAAACAGCCCCTGCTGCTCAGGTGTTAATTCCCTCCTAGAGGAGAAT
TTCACATCCACTGAGGAATCTTCCGAAGAAAACTTCAACTTGTTGGTGATCGAGGTGCAGTACCACCTGATGCTGCACAT
CCAGATGCAGGTGTGCAAGCTCCAGCTGTGGGACTGGCTAGCTGAGAGAAACAAACAGGGCCAAGAGTGTGTGGGCAAGT
TTGCCTGTCCTTAT
ORF - retro_ptro_1833 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.98 % |
| Parental protein coverage: | 65.08 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | GNSGVRKREEEGDGAGAVAAPPAID-FPAEGPDPKYDESDVPAELQVLKEPLQQPTFPFAVANQLLLVSL |
| G....R...EEG.G...VA.P.AID.FP.....P......VPAELQVLK.PLQQPTFPFAVANQL.L.SL | |
| Retrocopy | GCAAAREHKEEGHGVETVAVPSAID>FPPRAWTPNM--TYVPAELQVLK*PLQQPTFPFAVANQLPLISL |
| Parental | LEHLSHVHEPNPLRSRQVFKLLCQTFIK-MGLLSSFTCSDEFSSLRLHHNRAITHLMRSAKERVRQDPCE |
| ..HLSHV.EPNP..SRQVFKLLCQTF.K.MGLLSSFTC.D.FSSLRLHH.RAITHLMRS.KERV.QDPCE | |
| Retrocopy | VKHLSHVREPNPVHSRQVFKLLCQTFTK<MGLLSSFTC-DKFSSLRLHHHRAITHLMRSTKERVHQDPCE |
| Parental | DISHIQKIRSREVALEAQTSRYLNEFEELAILGKGGYGRVYKVRNKLDGQYYAIKKILIKGATKTVCMKV |
| .ISHIQKIRSREV..EAQTSRYLNEFEELAILGKGGYGRVYKVRNKLDGQYYAI.KILIKGATKT..MK. | |
| Retrocopy | AISHIQKIRSREVPFEAQTSRYLNEFEELAILGKGGYGRVYKVRNKLDGQYYAI*KILIKGATKTHYMKE |
| Parental | LREVKVLAGLQHPNIVGYHTAWIEHVHVIQPRADRAAIELPSLEVLSDQEEDREHCGVKNDESSSSSIIF |
| LR..KVLAGLQHPNI..YHTAW.EHV.V.QP.ADRA.I.LP.LEV.SDQ..DR...GVKN.E.SSS.IIF | |
| Retrocopy | LRGMKVLAGLQHPNIIRYHTAWTEHVQVVQPQADRASIQLPFLEVFSDQ-ADRYQYGVKNGENSSSPIIF |
| Parental | AEPTPE-KEKRFGESDTENQNNK-SVKYTTNLVIRDSGELESTLELQENGLAGLSASSIVEQQLPLR-RN |
| AE.T.E.KEK.F.ESDT.NQNNK..V.YT.N.V.RD..E.ES.LELQENGLAGLS..SIV.Q.L.LR..N | |
| Retrocopy | AELTSE<KEKPFAESDTQNQNNK<AVNYTINSVLRDTSEFESSLELQENGLAGLSTWSIVKQPLLLR>VN |
| Parental | SHLEESFTSTEESSEENFNFLGQTEAQYHLMLHIQMQLCELSLWDWIVERNKRGREYVDESACPY |
| S.LEE.FTSTEESSEENFN.L...E.QYHLMLHIQMQ.C.L.LWDW..ERNK.G.E.V...ACPY | |
| Retrocopy | SLLEENFTSTEESSEENFNLL-VIEVQYHLMLHIQMQVCKLQLWDWLAERNKQGQECVGKFACPY |
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_prefrontal_cortex | 0 .80 RPM | 72 .23 RPM |
| SRP007412_cerebellum | 1 .15 RPM | 94 .39 RPM |
| SRP007412_heart | 0 .29 RPM | 38 .74 RPM |
| SRP007412_kidney | 1 .15 RPM | 95 .32 RPM |
| SRP007412_liver | 0 .49 RPM | 82 .92 RPM |
| SRP007412_testis | 1 .48 RPM | 41 .42 RPM |
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1833 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1833 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ptro_1833 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2713 |
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000086232 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000000992 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000018904 | 1 retrocopy |
retro_ptro_1833 ,
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