RetrogeneDB ID:

retro_tbel_4125

Retrocopy
location
Organism:Treeshrew (Tupaia belangeri)
Coordinates:scaffold_68029:6013..6856(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSTBEG00000000905
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:EEF1A1
Ensembl ID:ENSTBEG00000012151
Aliases:None
Description:eukaryotic translation elongation factor 1 alpha 1 [Source:HGNC Symbol;Acc:3189]


Retrocopy-Parental alignment summary:






>retro_tbel_4125
GCCGACTGTGCTGTACTGATTGTTGCTGCTGGTGTTGGTGAATTTGAGGCTGGTATGTCCAAGAACAGGCAGACTCGTGA
GCATGCCCTTCTGGCTTACACACTGGGTGTGAAACAACTAATTGTTGGTGTTAACAAAATGGATTCTACTGAGACAACCT
ACAGTCAGAAGAGATGCAAGGAAATTGTTAAAGAAGTCGGCACCTACATTAAGAAAATATTACACAATTGGCTACAATCC
TGACATAGTAGCTTTTGTGCCTATTTCTTGTTGGAATGGTGATAACATGTTGGAGCCAAGTGCTAATATGCCGTGGTTCA
GGGGATGGAAAGTCACCCGTAAAGATGGCAATGCCAGTGGAACTACACTGCTCGAAGCTCTGGATTGCATCCTGTCACCA
ATTTGTCCAACTGACAAGCCCTTGTGTCTGCCCCTGCAGGATGTGTATAAAATTTGTGGTATTGGCACTGTCCTTGTCAG
CCGAGTGAAGACTGGCATGCTCAAATCTGGTATGGTGGTCACCTTTGCACCAGTCAATGTGACAACTGAAGTCAAGTTGG
TTGAAATGCACCATGAAGCTCTGAGTGAAGCTCTTCCTGGGGACAACGTGGGTTTCAATGTCAGGAATGTGCCTGTCAAA
GGTGTTCGATGTGGCCATGTTGCTGGTGACAGCAAAAATGACCCACCAATGGAAGCAGCTGGCTTCACTGCTCAGGTGAT
TATCCTGAACCATCCAGGCCAAATCAGTGTTGGCTATGCCCCTGTACTGGATTGTCACACAGCTCACATTGCTGCAAGTT
TGCTGAGCTGAAGGAAAAGATTGATCGCCGTTCTGGTAAAAAG

ORF - retro_tbel_4125 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.22 %
Parental protein coverage: 60.17 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalADCAVLIVAAGVGEFEAGISKNGQTREHALLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEI-VKEVSTY
ADCAVLIVAAGVGEFEAG.SKN.QTREHALLAYTLGVKQLIVGVNKMDSTE..YSQKR..EI..K.....
RetrocopyADCAVLIVAAGVGEFEAGMSKNRQTREHALLAYTLGVKQLIVGVNKMDSTETTYSQKRCKEI>LKKSAPT
ParentalIKK---IGYNPDTVAFVPISGWNGDNMLEPSANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDK
..K...IGYNPD.VAFVPIS.WNGDNMLEPSANMPWF.GWKVTRKDGNASGTTLLEALDCIL.P..PTDK
RetrocopyLRKYYTIGYNPDIVAFVPISCWNGDNMLEPSANMPWFRGWKVTRKDGNASGTTLLEALDCILSPICPTDK
ParentalPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKN
PL.LPLQDVYKI.GIGTV.V.RV.TG.LK.GMVVTFAPVNVTTEVK.VEMHHEALSEALPGDNVGFNV.N
RetrocopyPLCLPLQDVYKICGIGTVLVSRVKTGMLKSGMVVTFAPVNVTTEVKLVEMHHEALSEALPGDNVGFNVRN
ParentalVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYAPVLDCHTAHIA-CKFAELKEKIDRRS
V.VK.VR.G.VAGDSKNDPPMEAAGFTAQVIILNHPGQIS.GYAPVLDCHTAHIA.CKFAELKEKIDRRS
RetrocopyVPVKGVRCGHVAGDSKNDPPMEAAGFTAQVIILNHPGQISVGYAPVLDCHTAHIA<CKFAELKEKIDRRS
ParentalGKK
GKK
RetrocopyGKK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tupaia belangeri was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_tbel_4125 retrocopy.

TSS - click to see more details

Tupaia belangeri was not studied using FANTOM5 data.

Lab - click to see more details

retro_tbel_4125 was not experimentally validated.

Retrocopy orthology:
Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 11 parental genes, and 121 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000132491 retrocopy
retro_cfam_1007,
Equus caballus ENSECAG000000222601 retrocopy
retro_ecab_802,
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,
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,
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,
Tupaia belangeri ENSTBEG00000012151 51 retrocopies
retro_tbel_1084, retro_tbel_1330, retro_tbel_1373, retro_tbel_1452, retro_tbel_166, retro_tbel_1841, retro_tbel_1969, retro_tbel_1994, retro_tbel_2088, retro_tbel_2091, retro_tbel_2179, retro_tbel_2205, retro_tbel_2206, retro_tbel_2218, retro_tbel_2232, retro_tbel_2419, retro_tbel_2505, retro_tbel_259, retro_tbel_2627, retro_tbel_2718, retro_tbel_2738, retro_tbel_2758, retro_tbel_282, retro_tbel_2976, retro_tbel_3032, retro_tbel_3065, retro_tbel_3067, retro_tbel_3281, retro_tbel_3307, retro_tbel_3315, retro_tbel_338, retro_tbel_354, retro_tbel_360, retro_tbel_372, retro_tbel_3813, retro_tbel_3865, retro_tbel_3967, retro_tbel_4125 , retro_tbel_4192, retro_tbel_4282, retro_tbel_4352, retro_tbel_4370, retro_tbel_4466, retro_tbel_4496, retro_tbel_4639, retro_tbel_4660, retro_tbel_4695, retro_tbel_473, retro_tbel_588, retro_tbel_620, retro_tbel_903,
Tupaia belangeri ENSTBEG0000001717016 retrocopies
retro_tbel_1335, retro_tbel_1406, retro_tbel_2677, retro_tbel_2899, retro_tbel_2966, retro_tbel_3336, retro_tbel_348, retro_tbel_3485, retro_tbel_3658, retro_tbel_3727, retro_tbel_3948, retro_tbel_4091, retro_tbel_4127, retro_tbel_4290, retro_tbel_4507, retro_tbel_4527,
Drosophila melanogaster FBgn00005571 retrocopy
retro_dmel_9,


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