RetrogeneDB ID:

retro_ggor_2066

Retrocopy
location
Organism:Gorilla (Gorilla gorilla)
Coordinates:4:145005152..145006537(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSGGOG00000022861
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSGGOG00000025675
Aliases:None
Description:Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:G3S518]


Retrocopy-Parental alignment summary:






>retro_ggor_2066
ATGGGAAAGGAAAAAACTCATATCAACATTGTCGTCATTGGACATGTAGATTCAGGCAGGTCCACCACTACTGGCCATCT
GATCTACAAATGTAGTGGCATCGACAAAAGAACCATTGAAAAATTTGAGAAGGAGGCTGGCTGAGATGGGAAAGGGCTCC
TTCAAGTATGCCTGGGTCTTGGGTAAACTGAAAGCTGAGTGTGAACGTGGTATCACCATTGATATCTCCTTGTAGAAATT
TGAGACCAGCAGGTACTACATGGCTATCATTGATACCCCAGGACACAGAGACTTCATCAAAAACCTGATTACAGGGATAT
CTCAGGCTGACTGTAACGTCCTAAATGTTGCTGCTGGTGTTGGTGAATTTGAAGCTGGGAACTTCAAAAATGGGCAGACC
CGAGAGCATGCCCTTCTGGTTTACACACTGGGTGTGAACAACTAATCATTTGTGTTAACAAAATGGATTCCACTGAGCCA
CCTTACAGCCAGAAGAGATATCAGGGAATCGTTAAGGAAGTCAGCACTTACATTAAGAAATCGGCTACAACCCTGACACA
GTAGCGTTTGTGCCAATTTCTGGTTGGAATGTTGACAACATGCTGGAGCCAAGTGCTAACATGCCTTGGTTCAAGGGATG
GAAAGTCACCTGTAAGGATGGCAATACCAGTGGAACCACGCTGCTTGAGGCTCTGGACTGCATCCTATCACTGATTTGTC
CAACTGACAAGCCCACGTGCCTGACTCTTCAGGATGTCTACAAAATTGGTGGTATTGGTGCTGTTCCTGTAGGTCGAGTG
GAGACTGATGTTTTCAAACCTACTATGGTGGCCACCTTTGCTCCAGTCAACAATACAACTGAAGTAAAATCTGTCGAAAT
GCACCATGAAGCTTTGAGTGAAGCTCTTCCTGGGGACAATGTGGGCTTCAATGTCAAGAATGTGTCTGTCAAGGAGGTTC
ATCATGGCGATGTTGCTGGTGACAGCAAAAATGACCCACCAATGGAAGCAGCTGACTTCACTGCTCAAGTGATTATCCTG
AACCATTCAGGCCAAATCAGCGCTGGCTATGCCTCTGTACTGGATTGCCACATGGCTCACATTGCATGCCAGTTTGCTGA
GCTGAAGGAAAAGATTGATTGCCGTTCTGGTAAAAAGCTGGAAGATGGTCCTAAATTCTTGAAGTCTGGTGATGCTGCCA
TCATTGATATGGTTCCTGGCAAGCCTATGTGTGTTGAGAGCTTCTCAGACTATCCACCTCTGCATCGCTTTGCTGTTCAT
GATATGAGACAGACAGTTGTCCTGGGTGTCATCAAAGCAGTGGACAAGAAGGCTGCTGGAGCAGGCAAGGCCACTAAGTC
TGCTCAGAAAGCTTAGAAGGCCAAA

ORF - retro_ggor_2066 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.74 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 2
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEA-AEMGKGSFKYAWVLDKLKAERER
MGKEKTHINIVVIGHVDSG.STTTGHLIYKC.GIDKRTIEKFEKEA.AEMGKGSFKYAWVL.KLKAE.ER
RetrocopyMGKEKTHINIVVIGHVDSGRSTTTGHLIYKCSGIDKRTIEKFEKEA>AEMGKGSFKYAWVLGKLKAECER
ParentalGITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALL
GITIDISL.KFETS.YY..IID.PGHRDFIKN.ITG.SQADC.VL.VAAGVGEFEAG..KNGQTREHALL
RetrocopyGITIDISL*KFETSRYYMAIIDTPGHRDFIKNLITGISQADCNVLNVAAGVGEFEAGNFKNGQTREHALL
ParentalAYTLGV-KQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKK-IGYNPDTVAFVPISGWNGDNMLEPSAN
.YTLGV..QLI..VNKMDSTEPPYSQKRY..IVKEVSTYIKK.IGYNPDTVAFVPISGWN.DNMLEPSAN
RetrocopyVYTLGV<EQLIICVNKMDSTEPPYSQKRYQGIVKEVSTYIKK<IGYNPDTVAFVPISGWNVDNMLEPSAN
ParentalMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMV
MPWFKGWKVT.KDGN.SGTTLLEALDCIL....PTDKP..L.LQDVYKIGGIG.VPVGRVET.V.KP.MV
RetrocopyMPWFKGWKVTCKDGNTSGTTLLEALDCILSLICPTDKPTCLTLQDVYKIGGIGAVPVGRVETDVFKPTMV
ParentalVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIIL
.TFAPVN.TTEVKSVEMHHEALSEALPGDNVGFNVKNVSVK.V..G.VAGDSKNDPPMEAA.FTAQVIIL
RetrocopyATFAPVNNTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKEVHHGDVAGDSKNDPPMEAADFTAQVIIL
ParentalNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSD
NH.GQISAGYA.VLDCH.AHIAC.FAELKEKID.RSGKKLEDGPKFLKSGDAAI.DMVPGKPMCVESFSD
RetrocopyNHSGQISAGYASVLDCHMAHIACQFAELKEKIDCRSGKKLEDGPKFLKSGDAAIIDMVPGKPMCVESFSD
ParentalYPPLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
YPPL.RFAV.DMRQTV..GVIKAVDKKAAGAGK.TKSAQKA.KAK
RetrocopyYPPLHRFAVHDMRQTVVLGVIKAVDKKAAGAGKATKSAQKA*KAK

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_prefrontal_cortex 0 .29 RPM 813 .64 RPM
SRP007412_cerebellum 0 .04 RPM 767 .71 RPM
SRP007412_heart 0 .06 RPM 312 .04 RPM
SRP007412_kidney 0 .41 RPM 4298 .85 RPM
SRP007412_liver 0 .32 RPM 2725 .93 RPM
SRP007412_testis 0 .21 RPM 1470 .18 RPM

ChIP-Seq - click to see more details

Gorilla gorilla was not studied using ChIP-Seq data.

EST - click to see more details

Gorilla gorilla was not studied using EST data.

TSS - click to see more details

Gorilla gorilla was not studied using FANTOM5 data.

Lab - click to see more details

retro_ggor_2066 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggor_2066 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2983
Macaca mulatta retro_mmul_1906
Parental genes homology:
Parental genes homology involve 13 parental genes, and 87 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000132491 retrocopy
retro_cfam_1007,
Dipodomys ordii ENSDORG000000096291 retrocopy
retro_dord_509,
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,
Gorilla gorilla ENSGGOG00000025675 20 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,
Monodelphis domestica ENSMODG000000185334 retrocopies
retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus ENSMUSG0000003774215 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,
Pongo abelii ENSPPYG000000167771 retrocopy
retro_pabe_12,
Ictidomys tridecemlineatus ENSSTOG000000076874 retrocopies
retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Drosophila melanogaster FBgn00005571 retrocopy
retro_dmel_9,


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