RetrogeneDB ID:

retro_ecab_1017

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:9:67670408..67671995(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSECAG00000002402
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KPNA2
Ensembl ID:ENSECAG00000020573
Aliases:None
Description:karyopherin alpha 2 (RAG cohort 1, importin alpha 1) [Source:HGNC Symbol;Acc:6395]


Retrocopy-Parental alignment summary:






>retro_ecab_1017
ATGTCCTCCAACGAGAATGCTAATTCCCCGGCTGCCCGCCTTAACAGATTCAAGAACAAGGGGAAAGACAGCACAGAAAT
GAGGCGGCGCCGAATAGAAGTTAATGTGGAGCTGAGGAAAGCTAAGAAAGATGACCAGATGCTGAAAAGGAGAAATGTAA
GCTCCTTTCCTGATGATGCTACTTCTCCGCTACAGGAAAACTGCAACAACCAGGGCACTGTAAATTGGTCTGTTGAGGAT
ATTGTCAAAGGCGTAAACAGCAACAATTTGGAAAGCCAGCTCCAAGCTACTCAAGCTGCTAGGAAACTGCTTTCTAGAGA
AAAACAGCCCCCCATAGACAACATAATCCGGGCTGGTTTGATTCCAAAATTTGTGTCCTTCTTGGGCAGAACTGATTGTA
GTCCCATTCAGTTTGAGTCTACTTGGGCCCTCACTAACATCGCTTCCGGGACATCAGAACAGACCAAGGCTGTGGTAGAG
GGAGGTGCTATCCCAGCATTCATTTCTCTGTTGGCATCTCCCCACGCCCACATCAGTGAACAAGCCGTATGGGCTCTAGG
AAACATTGCAGGTGATGGTTCGGTTTTCCGAGACTTGGTGATCAAGTATGGTGCAGTTGACCCGCTGTTGGCTCTTCTTG
CAGTTCCCGATATGTCATCTTTGGCATGTGGTTACTTACGTAATCTTACCTGGACACTTTCAAACCTTTGTCGCAACAAG
AATCCTGCACCCCCATTAGATGCTGTTGAGCAAATTCTTCCCACTTTAGTTCGTCTCCTGCATCATGATGATCCAGAAGT
ATTAGCAGATACCTGTTGGGCCATTTCCTACCTTACCGATGGTCCGAATGAACGGATTGAAATGGTCGTGAAAACAGGAT
TGGTACCCCAACTTGTAAAGCTTCTAGGATCTACTGAATTGCCAATTGTGACTCCTGCACTAAGAGCCATAGGAAATATT
GTCACTGGGACAGACGAACAGACTCAGGTTGTAATAGATGCAGGAGCACTTGCCATCTTTCCCAGCCTGCTAACGAACCC
CAAAACTAACATTCAGAAGGAAGCTACGTGGACAATGTCAAACATCACAGCTGGCCGCCAGGACCAGATACAGCAAGTTG
TGAATCATGGATTAGTCCCATTCCTCATTGGTGTTCTCTCTAAGGCAGACTTTAAGACACAAAAGGAAGCTGTATGGGCT
GTGACCAACTATACAAGTGGTAGAACAGTTGAACAGATTGTATACCTTGTTCATTGTGGCATAATAGAACCGTTGATGAA
CCTCTTAACTGCAAAAGACACCAAAATTATTCTGGTTATTCTGGATGCCATTTCAAATATCTTTCAGGCTGCTGAGAAAC
TAGGTGAAACTGAGAAACTTAGTATAATGATTGAAGAATGTGGAGGTCTGGACAAAATTGAAGCTCTACAAAACCATGAA
AATGAGTCTGTGTACAAAGCTTTGTTAAACTTGATTGAGAAGTATTTCTCTGTAGAGGAAGAGGAAGATGAAAATGTTGT
GCCAGAAACTACCTCTGAAGGCTATACATTCCAAGTTCAGGATGGCCCTCCGGGGACCTTTAACTTT

ORF - retro_ecab_1017 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.49 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMSSNENANSPAARLNRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQENRNN
MSSNENANSPAARLNRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQEN.NN
RetrocopyMSSNENANSPAARLNRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQENCNN
ParentalQGTVNWSVEDIVKGVNSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGRTDCSPIQFES
QGTVNWSVEDIVKGVNSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGRTDCSPIQFES
RetrocopyQGTVNWSVEDIVKGVNSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGRTDCSPIQFES
ParentalAWALTNIASGTSEQTKAVVEGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPLL
.WALTNIASGTSEQTKAVVEGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPLL
RetrocopyTWALTNIASGTSEQTKAVVEGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPLL
ParentalALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTD
ALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTD
RetrocopyALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTD
ParentalGPNERIEMVVKTGVVPQLVKLLGSTELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAIFPSLLTNPKTN
GPNERIEMVVKTG.VPQLVKLLGSTELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAIFPSLLTNPKTN
RetrocopyGPNERIEMVVKTGLVPQLVKLLGSTELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAIFPSLLTNPKTN
ParentalIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCG
IQKEATWTMSNITAGRQDQIQQVVNHGLVPFL.GVLSKADFKTQKEAVWAVTNYTSG.TVEQIVYLVHCG
RetrocopyIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLIGVLSKADFKTQKEAVWAVTNYTSGRTVEQIVYLVHCG
ParentalIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKASLN
IIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKA.LN
RetrocopyIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKALLN
ParentalLIEKYFSVEEEEDQNVVPETTSEGYTFQVQDGPPGTFDF
LIEKYFSVEEEED.NVVPETTSEGYTFQVQDGPPGTF.F
RetrocopyLIEKYFSVEEEEDENVVPETTSEGYTFQVQDGPPGTFNF

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
SRP021940_articular_cartilage 0 .00 RPM 0 .77 RPM
SRP021940_cerebellum 0 .52 RPM 1 .45 RPM
SRP021940_embryo 1 .64 RPM 19 .77 RPM
SRP021940_placental_villous 0 .19 RPM 5 .87 RPM
SRP021940_synovial_membrane 0 .22 RPM 2 .66 RPM
SRP021940_testis 3 .71 RPM 35 .49 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_1017 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_1017 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_1017 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184113 retrocopies
retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus ENSBTAG000000122251 retrocopy
retro_btau_1830,
Canis familiaris ENSCAFG000000115982 retrocopies
retro_cfam_648, retro_cfam_90,
Cavia porcellus ENSCPOG000000263181 retrocopy
retro_cpor_46,
Dasypus novemcinctus ENSDNOG000000191516 retrocopies
retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus ENSECAG000000005541 retrocopy
retro_ecab_981,
Equus caballus ENSECAG00000020573 2 retrocopies
retro_ecab_1017 , retro_ecab_1123,
Echinops telfairi ENSETEG000000044452 retrocopies
retro_etel_346, retro_etel_347,
Felis catus ENSFCAG000000019362 retrocopies
retro_fcat_1176, retro_fcat_921,
Myotis lucifugus ENSMLUG000000279467 retrocopies
retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta ENSMMUG000000182563 retrocopies
retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica ENSMODG000000038971 retrocopy
retro_mdom_271,
Mus musculus ENSMUSG000000183621 retrocopy
retro_mmus_229,
Oryctolagus cuniculus ENSOCUG000000159134 retrocopies
retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii ENSOGAG000000276727 retrocopies
retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii ENSPPYG000000085691 retrocopy
retro_pabe_3501,
Rattus norvegicus ENSRNOG000000153291 retrocopy
retro_rnor_42,
Sarcophilus harrisii ENSSHAG000000113911 retrocopy
retro_shar_165,


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