RetrogeneDB ID:

retro_pabe_2621

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:16295352..16296451(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTG1
Ensembl ID:ENSPPYG00000008735
Aliases:None
Description:actin, gamma 1 [Source:HGNC Symbol;Acc:144]


Retrocopy-Parental alignment summary:






>retro_pabe_2621
GAAGAAGAGTTCGCTGCACTTCTCATTGACAATGGCTCTAGCATGTGCAAAGCTGGCTTTGCTGGGGGAGCTGTTTTCCC
CTCCATCGTCTGGCACCCCTGGTACCAGCACGTGTTGGTGGGCATGGGCCAGAAGGACTCCTACTTGAGTGACAAAGCCC
AGAGCAAGCGCAGCATCCTGACCCTGAAGTACCCCATCGAGCATGGCATTGTCACTAACTGGGACGACATGGAGAAGAGC
TGGCACTACACCTTCTACAAGGAGCTGCGCATGGCCCCAGAGGAGCACACGGTGCTGCTGACTGAGGCCCCTCTGAACCC
CAAGGCCAACAGAGAAGATGACTCAGATCATGTTTGAGACCTTCAACACCCCAGCCATGTACGTGGCCATCCAGGCCAGT
GCTGTCCCTCTACACCTCCGGGCACGCCACTGGCATTTTCATGAACTCTGGAGATGGGGTCACCCACACGGTGCTCATCT
ACAAGGGCTATACTGTCCTCCATGCCATCCTGCCTCTGGACCTAGCTGGCTGGGACCTGACCCACTACCTTATGAAGATC
CTCACCAAGCACGACTACAGCTTCACCACCACCACCAAGAGGTAGATCATGCGTGACATCGAGGAGAAGCTGTGCTACCT
CAACCTGGACTTGGAGCAGGATATGGCCACCACCGCATACTCCTCCTCCCTGGAGAAGAGCTACAAGCTGCCTGATGGCC
AGGTCATCACCACTGGCACCGAGCAGTTCCAGTGTCTGGAGGCACTGTTCCAGCCTTCCTTCCTGAGCAGGGAATCTTGC
TGCATCAGGAGACCACCTTCAACTCCATCATGAAGTGTGACATGGACATCCACAAAGACCTGTACGCCAACACGGTGCTG
TCCAGCAGCACCACAATGTACGTGGGTATCGCCCACAGTATGCAGAAGGAGATCATCGCCCTGGCACCCAGCACCATGAA
GATCAAGATCATCGCACCCCCAGAGTGCAAGTACTTGGTGTGAATCGGCAGCTCCATCCTGGCCTCACTGTCCACCTTCC
AGGAGATGTGGATTAGCAAGCAGGAGTATGACGAGTCAGTACCCCCACGCCCCCATCGT

ORF - retro_pabe_2621 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.54 %
Parental protein coverage: 98.93 %
Number of stop codons detected: 2
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPI
EEE.AAL.IDNGS.MCKAGFAG.....AVFPSIV..P..Q.V.VGMGQKDSY..D.AQSKR.ILTLKYPI
RetrocopyEEEFAALLIDNGSSMCKAGFAGG----AVFPSIVWHPWYQHVLVGMGQKDSYLSDKAQSKRSILTLKYPI
ParentalEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLN-PKANREKMTQIMFETFNTPAMYVAIQA-V
EHGIVTNWDDMEK.WH.TFY.ELR.APEEH.VLLTEAPLN.P....EKMTQIMFETFNTPAMYVAIQA.V
RetrocopyEHGIVTNWDDMEKSWHYTFYKELRMAPEEHTVLLTEAPLN>PRPT-EKMTQIMFETFNTPAMYVAIQA>V
ParentalLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIV
LSLY.SG..TGI.M.SGDGVTHTV.IY.GY...HAIL.LDLAG.DLT.YLMKILT...YSFTTT..R.I.
RetrocopyLSLYTSGHATGIFMNSGDGVTHTVLIYKGYTVLHAILPLDLAGWDLTHYLMKILTKHDYSFTTTTKR*IM
ParentalRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGI-HETT
RDI.EKLCY..LD.EQ.MAT.A.SSSLEKSY.LPDGQVIT.G.E.F.C.EALFQPSFL..ESC.I..ETT
RetrocopyRDIEEKLCYLNLDLEQDMATTAYSSSLEKSYKLPDGQVITTGTEQFQCLEALFQPSFLSRESCCI<QETT
ParentalFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS
FNSIMKCD.DI.KDLYANTVLS..TTMY.GIA..MQKEI.ALAPSTMKIKIIAPPE.KY.V.IG.SILAS
RetrocopyFNSIMKCDMDIHKDLYANTVLSSSTTMYVGIAHSMQKEIIALAPSTMKIKIIAPPECKYLV*IGSSILAS
ParentalLSTFQQMWISKQEYDESGPSIVHR
LSTFQ.MWISKQEYDES.P...HR
RetrocopyLSTFQEMWISKQEYDESVPPRPHR

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 .00 RPM 426 .62 RPM
SRP007412_cerebellum 0 .00 RPM 117 .22 RPM
SRP007412_heart 0 .03 RPM 145 .94 RPM
SRP007412_kidney 0 .00 RPM 354 .54 RPM
SRP007412_liver 0 .00 RPM 440 .45 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_2621 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2621 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2621 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2122
Parental genes homology:
Parental genes homology involve 25 parental genes, and 88 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000152383 retrocopies
retro_acar_176, retro_acar_199, retro_acar_7,
Ailuropoda melanoleuca ENSAMEG000000160151 retrocopy
retro_amel_929,
Callithrix jacchus ENSCJAG000000028853 retrocopies
retro_cjac_139, retro_cjac_336, retro_cjac_377,
Cavia porcellus ENSCPOG000000121011 retrocopy
retro_cpor_361,
Equus caballus ENSECAG000000186001 retrocopy
retro_ecab_98,
Felis catus ENSFCAG000000264342 retrocopies
retro_fcat_257, retro_fcat_377,
Homo sapiens ENSG0000018400910 retrocopies
retro_hsap_1548, retro_hsap_1607, retro_hsap_2405, retro_hsap_2591, retro_hsap_2605, retro_hsap_3466, retro_hsap_3631, retro_hsap_409, retro_hsap_4818, retro_hsap_4935,
Gallus gallus ENSGALG000000287491 retrocopy
retro_ggal_6,
Gorilla gorilla ENSGGOG000000140436 retrocopies
retro_ggor_1495, retro_ggor_2338, retro_ggor_2449, retro_ggor_273, retro_ggor_413, retro_ggor_520,
Loxodonta africana ENSLAFG000000091671 retrocopy
retro_lafr_116,
Monodelphis domestica ENSMODG000000026473 retrocopies
retro_mdom_187, retro_mdom_59, retro_mdom_89,
Mustela putorius furoENSMPUG000000116101 retrocopy
retro_mputfur_279,
Mus musculus ENSMUSG000000628257 retrocopies
retro_mmus_1043, retro_mmus_1524, retro_mmus_2383, retro_mmus_3128, retro_mmus_3265, retro_mmus_3607, retro_mmus_3705,
Nomascus leucogenys ENSNLEG000000155063 retrocopies
retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Petromyzon marinus ENSPMAG000000041611 retrocopy
retro_pmar_4,
Pongo abelii ENSPPYG000000024591 retrocopy
retro_pabe_3027,
Pongo abelii ENSPPYG000000026051 retrocopy
retro_pabe_1930,
Pongo abelii ENSPPYG000000063181 retrocopy
retro_pabe_1317,
Pongo abelii ENSPPYG00000008735 11 retrocopies
retro_pabe_1091, retro_pabe_1391, retro_pabe_1727, retro_pabe_2187, retro_pabe_2308, retro_pabe_2621 , retro_pabe_2945, retro_pabe_3381, retro_pabe_3475, retro_pabe_3760, retro_pabe_600,
Pongo abelii ENSPPYG0000001733623 retrocopies
retro_pabe_1281, retro_pabe_1292, retro_pabe_1575, retro_pabe_1610, retro_pabe_1772, retro_pabe_1816, retro_pabe_1911, retro_pabe_2042, retro_pabe_2168, retro_pabe_2175, retro_pabe_2188, retro_pabe_227, retro_pabe_2754, retro_pabe_2811, retro_pabe_2824, retro_pabe_2862, retro_pabe_2978, retro_pabe_309, retro_pabe_3563, retro_pabe_3567, retro_pabe_3746, retro_pabe_745, retro_pabe_86,
Pelodiscus sinensis ENSPSIG000000021022 retrocopies
retro_psin_25, retro_psin_4,
Rattus norvegicus ENSRNOG000000367011 retrocopy
retro_rnor_715,
Sus scrofa ENSSSCG000000283551 retrocopy
retro_sscr_389,
Ictidomys tridecemlineatus ENSSTOG000000068682 retrocopies
retro_itri_1675, retro_itri_531,
Xenopus tropicalis ENSXETG000000251161 retrocopy
retro_xtro_6,


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