RetrogeneDB ID:

retro_mmus_1518

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:16:51362452..51363831(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000081453
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Eef1a1
Ensembl ID:ENSMUSG00000037742
Aliases:None
Description:eukaryotic translation elongation factor 1 alpha 1 [Source:MGI Symbol;Acc:MGI:1096881]


Retrocopy-Parental alignment summary:






>retro_mmus_1518
ATGGGAAAGGAAAAGACTCACATCAACATCGTTGTAATCGGACACGTAGATTCCGGCAAGTCCACCACAACCGGCCACCT
GATCTACAAATGTGGTGCAATCGATAAGCGAACCATCGAAAAGTTTGAGAAGGAGGCTGCTGAGATGGGAAAGTGCTCCT
TCAAGTATGCCTGGGTCTTAGACAAATTGAAAACTGAGCCTGAGCGTAGTATCACTATTGACATCTCCTGTGGAAATTCA
AGGCCAGCAAATACTATGTGACCATCATTGATGCCCTAGGACACGGAGACTTCATCAAAAACATGATTACAGGCACATCC
CAGGCAGACTGTGCTTTCCTGATTGTTGCTGCTGGTTGTTGGTGAATTTGAAGCTGGTATCTCCAAGAACGGGCAGACTC
GCGAGCATGCTCTTCTGGCTTACACCCTGGGTGTGAAACAGCTGATTGTTGGTATCAACAAAATGGATTCCACCGAGCCA
CCATACAGTCAGAAGAGATACGAGGAAATCGTTAAGGAAGTCAGCACCTACATTAAGAAAATTGGCTACAACCCTGACAC
AGTAGCATTTGTGCCAATTTCTGGTTGGAATGGTGACAACATGCTGGAGCCAAGTGCTAATATGCCTTGGTTCAAGGGAT
GGAAAATCACCCACAAAGATGGCAGTGCCAGTGCACCACACTGCTGGAAGCTTTGAATTGTATCCTACCACCAACTCGTC
CAACTGACAAGCCTCTGCGACTACCCCTCCAGGATAAAATTGGAGGCATTGGCACTATCCCTGTGGGCAGAGTGGAGACT
GGTGTTCTCAAACCTGGCATGGTGGTTACCTTTGCTCCAGTCAATGTAATAACTGAAGTCAAGTCTGTTGAAATGCACCA
TGAAGCTTTGAGTGAAGCTCTTCCTGGGGACAATATGGGCTTCAATGTAAAGAACGTGTAGGTCAAAGGTATTAGACAAG
GCAATGTTGCTGATGACAGCAAAAACGACCTACCAATGGAAGCAGCTGGCTTCACTGCTCAGGTGATTATCCTGAACCAT
CCAGGCCAAATCAGTGCTGGCTATGCTCCTGTTCTGGATTGTCACACAGCCCACATAGCATGCAAGTTTGCTGAGCTTAA
AGAAAAGATCGATAGTCGTTCTGGTAAGAAGCTGGAAGATGGCCCCAAATTCCTGAAGTCTGGTGATGCAGCCATTGTTG
ATATGGTCCCTGGCAAGCCCACGTGTGTTGAGAGCTTCTCTGACTATCTGCCACTTGGTCGTTTTGCTGTTCGTGACATG
AGGCAGACAGTTGCTGTGGGTGTCATCAAAGCTGTGGACAAGAAGGCTGCTGGAGCTGCCAAAGTCACCAAGTCTGCCTA
GAAAACTCAGAAGGCTAAA

ORF - retro_mmus_1518 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.47 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCG.IDKRTIEKFEKEAAEMGK.SFKYAWVLDKLK.E.ER.
RetrocopyMGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGAIDKRTIEKFEKEAAEMGKCSFKYAWVLDKLKTEPERS
ParentalITIDIS-LWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAG-VGEFEAGISKNGQTREHAL
ITIDIS.LWKF..SKYYVTIIDA.GH.DFIKNMITGTSQADCA.LIVAAG.VGEFEAGISKNGQTREHAL
RetrocopyITIDIS<LWKFKASKYYVTIIDALGHGDFIKNMITGTSQADCAFLIVAAG>VGEFEAGISKNGQTREHAL
ParentalLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANM
LAYTLGVKQLIVG.NKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANM
RetrocopyLAYTLGVKQLIVGINKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANM
ParentalPWFKGWKVTRKDGSASG-TTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMV
PWFKGWK.T.KDGSAS..TTLLEAL.CILPPTRPTDKPLRLPLQD..KIGGIGT.PVGRVETGVLKPGMV
RetrocopyPWFKGWKITHKDGSASA<TTLLEALNCILPPTRPTDKPLRLPLQD--KIGGIGTIPVGRVETGVLKPGMV
ParentalVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIIL
VTFAPVNV.TEVKSVEMHHEALSEALPGDN.GFNVKNV.VK..R.GNVA.DSKND.PMEAAGFTAQVIIL
RetrocopyVTFAPVNVITEVKSVEMHHEALSEALPGDNMGFNVKNV*VKGIRQGNVADDSKNDLPMEAAGFTAQVIIL
ParentalNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSD
NHPGQISAGYAPVLDCHTAHIACKFAELKEKID.RSGKKLEDGPKFLKSGDAAIVDMVPGKP.CVESFSD
RetrocopyNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDSRSGKKLEDGPKFLKSGDAAIVDMVPGKPTCVESFSD
ParentalYPPLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
Y.PLGRFAVRDMRQTVAVGVIKAVDKKAAGA.KVTKSA.K.QKAK
RetrocopyYLPLGRFAVRDMRQTVAVGVIKAVDKKAAGAAKVTKSA*KTQKAK

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 .49 RPM 938 .67 RPM
SRP007412_cerebellum 0 .30 RPM 652 .71 RPM
SRP007412_heart 0 .37 RPM 465 .27 RPM
SRP007412_kidney 1 .52 RPM 1781 .75 RPM
SRP007412_liver 0 .93 RPM 2430 .48 RPM
SRP007412_testis 0 .46 RPM 1060 .92 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1518 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1518 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_48089115 libraries195 libraries713 libraries39 libraries10 libraries

The graphical summary, for retro_mmus_1518 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_1518 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1518 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 29 parental genes, and 226 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000778614 retrocopies
retro_amel_1064, retro_amel_1072, retro_amel_1079, retro_amel_1140, retro_amel_1167, retro_amel_1203, retro_amel_1227, retro_amel_1283, retro_amel_1371, retro_amel_160, retro_amel_1742, retro_amel_1797, retro_amel_1855, retro_amel_200,
Bos taurus ENSBTAG000000145343 retrocopies
retro_btau_114, retro_btau_115, retro_btau_192,
Canis familiaris ENSCAFG000000122221 retrocopy
retro_cfam_1478,
Canis familiaris ENSCAFG000000132491 retrocopy
retro_cfam_1007,
Callithrix jacchus ENSCJAG000000100516 retrocopies
retro_cjac_1431, retro_cjac_3075, retro_cjac_34, retro_cjac_3735, retro_cjac_733, retro_cjac_97,
Cavia porcellus ENSCPOG0000000406715 retrocopies
retro_cpor_1150, retro_cpor_1162, retro_cpor_1191, retro_cpor_1256, retro_cpor_1393, retro_cpor_1492, retro_cpor_1499, retro_cpor_348, retro_cpor_381, retro_cpor_387, retro_cpor_413, retro_cpor_709, retro_cpor_891, retro_cpor_918, retro_cpor_959,
Dipodomys ordii ENSDORG000000096291 retrocopy
retro_dord_509,
Equus caballus ENSECAG000000203632 retrocopies
retro_ecab_66, retro_ecab_93,
Equus caballus ENSECAG000000222601 retrocopy
retro_ecab_802,
Erinaceus europaeus ENSEEUG000000003423 retrocopies
retro_eeur_407, retro_eeur_492, retro_eeur_625,
Echinops telfairi ENSETEG0000000423614 retrocopies
retro_etel_1189, retro_etel_1248, retro_etel_1260, retro_etel_1429, retro_etel_1436, retro_etel_1472, retro_etel_1578, retro_etel_1602, retro_etel_1682, retro_etel_1808, retro_etel_2135, retro_etel_366, retro_etel_411, retro_etel_830,
Felis catus ENSFCAG0000003097714 retrocopies
retro_fcat_1021, retro_fcat_1388, retro_fcat_1569, retro_fcat_1683, retro_fcat_1825, retro_fcat_184, retro_fcat_1915, retro_fcat_220, retro_fcat_221, retro_fcat_334, retro_fcat_515, retro_fcat_566, retro_fcat_688, retro_fcat_737,
Gorilla gorilla ENSGGOG0000002567520 retrocopies
retro_ggor_1193, retro_ggor_1258, retro_ggor_1305, retro_ggor_1444, retro_ggor_1529, retro_ggor_20, retro_ggor_2006, retro_ggor_2021, retro_ggor_2056, retro_ggor_2066, retro_ggor_2205, retro_ggor_2526, retro_ggor_2637, retro_ggor_2826, retro_ggor_322, retro_ggor_375, retro_ggor_790, retro_ggor_860, retro_ggor_919, retro_ggor_978,
Loxodonta africana ENSLAFG000000280811 retrocopy
retro_lafr_651,
Microcebus murinus ENSMICG0000001531921 retrocopies
retro_mmur_1027, retro_mmur_1116, retro_mmur_1145, retro_mmur_1182, retro_mmur_1190, retro_mmur_12, retro_mmur_1282, retro_mmur_1316, retro_mmur_1339, retro_mmur_1343, retro_mmur_1350, retro_mmur_1568, retro_mmur_171, retro_mmur_26, retro_mmur_273, retro_mmur_49, retro_mmur_682, retro_mmur_729, retro_mmur_825, retro_mmur_877, retro_mmur_9,
Myotis lucifugus ENSMLUG0000001353724 retrocopies
retro_mluc_110, retro_mluc_1252, retro_mluc_1392, retro_mluc_1430, retro_mluc_1558, retro_mluc_1628, retro_mluc_1644, retro_mluc_1853, retro_mluc_1901, retro_mluc_1910, retro_mluc_2071, retro_mluc_2148, retro_mluc_2154, retro_mluc_2277, retro_mluc_2355, retro_mluc_2358, retro_mluc_2359, retro_mluc_2391, retro_mluc_441, retro_mluc_470, retro_mluc_677, retro_mluc_950, retro_mluc_956, retro_mluc_966,
Macaca mulatta ENSMMUG0000000485215 retrocopies
retro_mmul_1375, retro_mmul_1407, retro_mmul_1518, retro_mmul_1525, retro_mmul_1690, retro_mmul_1707, retro_mmul_1721, retro_mmul_1739, retro_mmul_1743, retro_mmul_1906, retro_mmul_2196, retro_mmul_2250, retro_mmul_323, retro_mmul_6, retro_mmul_848,
Monodelphis domestica ENSMODG000000185334 retrocopies
retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mustela putorius furoENSMPUG000000038166 retrocopies
retro_mputfur_1514, retro_mputfur_1643, retro_mputfur_220, retro_mputfur_502, retro_mputfur_844, retro_mputfur_862,
Mustela putorius furoENSMPUG0000000427110 retrocopies
retro_mputfur_1179, retro_mputfur_1276, retro_mputfur_1351, retro_mputfur_1394, retro_mputfur_284, retro_mputfur_355, retro_mputfur_474, retro_mputfur_678, retro_mputfur_920, retro_mputfur_973,
Mus musculus ENSMUSG00000037742 15 retrocopies
retro_mmus_1349, retro_mmus_1518 , retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Nomascus leucogenys ENSNLEG000000014766 retrocopies
retro_nleu_1492, retro_nleu_1584, retro_nleu_1754, retro_nleu_1901, retro_nleu_235, retro_nleu_829,
Oryctolagus cuniculus ENSOCUG000000084813 retrocopies
retro_ocun_1102, retro_ocun_187, retro_ocun_71,
Otolemur garnettii ENSOGAG0000000915210 retrocopies
retro_ogar_1215, retro_ogar_1622, retro_ogar_1779, retro_ogar_1840, retro_ogar_2281, retro_ogar_2526, retro_ogar_2557, retro_ogar_3013, retro_ogar_3046, retro_ogar_3271,
Pongo abelii ENSPPYG000000167771 retrocopy
retro_pabe_12,
Pan troglodytes ENSPTRG000000183471 retrocopy
retro_ptro_71,
Ictidomys tridecemlineatus ENSSTOG000000076874 retrocopies
retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Vicugna pacos ENSVPAG000000076379 retrocopies
retro_vpac_369, retro_vpac_404, retro_vpac_510, retro_vpac_511, retro_vpac_523, retro_vpac_544, retro_vpac_582, retro_vpac_592, retro_vpac_606,
Drosophila melanogaster FBgn00005571 retrocopy
retro_dmel_9,




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