RetrogeneDB - Retrocopy retro_vpac

                        
>retro_vpac_351
ATGGCGGAGGTACTGCCAGCTGACTCCCGGAAACTGCTACACCCGCTGAATGCCCTGCTGGGACAGGAGCCGAGATGTCA

GCCAAAGGTCTGCGGCTTGAGACTGGATTCTGCCCATGATAATGGCCTTAGAATGACTGCACGACTAAGAAGCTTTGAAG

TAAAAGATCTTGGTCCGACTCAGTTCTTTGGCTTTGACACAGAGACGTTTTCTCTAGCTGTGAATTTACTGGACAGATTT

CCTGTTAAAAATGAAGGTACAGCCCAAGCACCTGGGGTGTGTTGGACTGAGTGGCTTCTACTTGGCTGTAAAATCAACAG

AAGAGGAAAGGAATGTCCCGTTGGCAACTGACTTGATCCGAATAAGCCAATATAGGTTCAGGGTTTCAGACTTGATGAGA

ATGGAAAAGATCGTGTTGGAGAAGGTGTGTTGGAAAGTCAAAGCTCCAACTGCCTTTCAATTTCTACAACTCTGTTATTC

ACTCACTCAAGAGAACGTGTCACATGAAAGGAAGAGCAGCCTTAATTTTGAAAGACTAGCAGCCTAACTTGAGGCATGCT

ACTGCAGGATCACAGCTTCTAAAGCCAGGCCGTCTGCGTTGGCACTGTCTATCACTGCATCGCAGATCAAGCACAGACGC

GTGTACAGTTAACGGAAAGAGTAGAGAATCTTCAGAGCCATTCCAAGATGAATGGCAGAGATCTGACTTTCTGGCAAGAG

CTCGCATCTAAGTGTTTAACTGAACATGCATCAAACAAGTGTTGCAAACCAAATATTCAGAAGTTGAAATGGATTGTTTC

TGGGCGGACTGCACGGCAACTGAAGCATAGTTACTACAGGATAACCCACCTTCCAACAATTCCTGAAACGGGCCCT

ORF - retro_vpac_351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	83.5 %
Parental protein coverage:	100.0 %
Number of stop codons detected:	1
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalMIEVLTTTDSQKLLHQLNALLEQETRCQPKVCGLRLIESAHDNGLRMTARLRDFEVKDLLSLTQFFGFDT
M.EVL...DS.KLLH.LNALL.QE.RCQPKVCGLRL..SAHDNGLRMTARLR.FEVKDL...TQFFGFDT
RetrocopyMAEVLPA-DSRKLLHPLNALLGQEPRCQPKVCGLRL-DSAHDNGLRMTARLRSFEVKDL-GPTQFFGFDT
ParentalETFSLAVNLLDRF-LSKMKVQPKHLGCVGLSCFYLAVKSIEEERNVPLATDLIRISQYRFTVSDLMRMEK
ETFSLAVNLLDRF.L.KMKVQPKHLGCVGLS.FYLAVKS.EEERNVPLATDLIRISQYRF.VSDLMRMEK
RetrocopyETFSLAVNLLDRF>LLKMKVQPKHLGCVGLSGFYLAVKSTEEERNVPLATDLIRISQYRFRVSDLMRMEK
ParentalIVLEKVCWKVKATTAFQFLQLYYSLIQENLPHERKTILNFERLEAQLKACYCRIIFSKAKPSVLALSIIA
IVLEKVCWKVKA.TAFQFLQL.YSL.QEN..HERK..LNFERL.A.L.ACYCRI..SKA.PS.LALSI.A
RetrocopyIVLEKVCWKVKAPTAFQFLQLCYSLTQENVSHERKSSLNFERLAA*LEACYCRITASKARPSALALSITA
ParentalLEI-QAQKCVELTERIEHLQKHSKINGRDLTFWQELVSKCLTEYASNKCSKPNVQKLKWIVSGRTARQLK
..I.QAQ..V.LTER.E.LQ.HSK.NGRDLTFWQEL.SKCLTE.ASNKC.KPN.QKLKWIVSGRTARQLK
RetrocopySQI<QAQTRVQLTERVENLQSHSKMNGRDLTFWQELASKCLTEHASNKCCKPNIQKLKWIVSGRTARQLK
ParentalHSYYRITHLPTIPEMGP
HSYYRITHLPTIPE.GP
RetrocopyHSYYRITHLPTIPETGP

                            

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

                        

RNA-Seq - click to see more details

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Vicugna pacos was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_vpac_351 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_351 was not experimentally validated.

Retrocopy orthology:

Vicugna pacos 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006607	2 retrocopies	retro_btau_1064, retro_btau_763,
Canis familiaris	ENSCAFG00000017207	1 retrocopy	retro_cfam_1657,
Callithrix jacchus	ENSCJAG00000015341	1 retrocopy	retro_cjac_2319,
Dipodomys ordii	ENSDORG00000014293	1 retrocopy	retro_dord_486,
Equus caballus	ENSECAG00000018880	1 retrocopy	retro_ecab_152,
Felis catus	ENSFCAG00000027366	1 retrocopy	retro_fcat_763,
Myotis lucifugus	ENSMLUG00000001667	1 retrocopy	retro_mluc_1341,
Monodelphis domestica	ENSMODG00000007651	1 retrocopy	retro_mdom_1018,
Mus musculus	ENSMUSG00000020326	1 retrocopy	retro_mmus_1534,
Oryctolagus cuniculus	ENSOCUG00000002129	3 retrocopies	retro_ocun_1287, retro_ocun_512, retro_ocun_615,
Otolemur garnettii	ENSOGAG00000007639	1 retrocopy	retro_ogar_2452,
Pteropus vampyrus	ENSPVAG00000017902	1 retrocopy	retro_pvam_1027,
Sarcophilus harrisii	ENSSHAG00000007465	2 retrocopies	retro_shar_328, retro_shar_490,
Vicugna pacos	ENSVPAG00000008340	1 retrocopy	retro_vpac_351 ,
Vicugna pacos	ENSVPAG00000011865	1 retrocopy	retro_vpac_197,

	RetrogeneDB ID:	retro_vpac_351
Retrocopy location	Organism:	*Alpaca (Vicugna pacos)*
	Coordinates:	scaffold_113855:257..1133(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	CCNG1
	Ensembl ID:	ENSVPAG00000008340
	Aliases:	None
	Description:	cyclin G1 [Source:HGNC Symbol;Acc:1592]

Parental	MIEVLTTTDSQKLLHQLNALLEQETRCQPKVCGLRLIESAHDNGLRMTARLRDFEVKDLLSLTQFFGFDT
	M.EVL...DS.KLLH.LNALL.QE.RCQPKVCGLRL..SAHDNGLRMTARLR.FEVKDL...TQFFGFDT
Retrocopy	MAEVLPA-DSRKLLHPLNALLGQEPRCQPKVCGLRL-DSAHDNGLRMTARLRSFEVKDL-GPTQFFGFDT

Parental	ETFSLAVNLLDRF-LSKMKVQPKHLGCVGLSCFYLAVKSIEEERNVPLATDLIRISQYRFTVSDLMRMEK
	ETFSLAVNLLDRF.L.KMKVQPKHLGCVGLS.FYLAVKS.EEERNVPLATDLIRISQYRF.VSDLMRMEK
Retrocopy	ETFSLAVNLLDRF>LLKMKVQPKHLGCVGLSGFYLAVKSTEEERNVPLATDLIRISQYRFRVSDLMRMEK

Parental	IVLEKVCWKVKATTAFQFLQLYYSLIQENLPHERKTILNFERLEAQLKACYCRIIFSKAKPSVLALSIIA
	IVLEKVCWKVKA.TAFQFLQL.YSL.QEN..HERK..LNFERL.A.L.ACYCRI..SKA.PS.LALSI.A
Retrocopy	IVLEKVCWKVKAPTAFQFLQLCYSLTQENVSHERKSSLNFERLAA*LEACYCRITASKARPSALALSITA

Parental	LEI-QAQKCVELTERIEHLQKHSKINGRDLTFWQELVSKCLTEYASNKCSKPNVQKLKWIVSGRTARQLK
	..I.QAQ..V.LTER.E.LQ.HSK.NGRDLTFWQEL.SKCLTE.ASNKC.KPN.QKLKWIVSGRTARQLK
Retrocopy	SQI<QAQTRVQLTERVENLQSHSKMNGRDLTFWQELASKCLTEHASNKCCKPNIQKLKWIVSGRTARQLK

Parental	HSYYRITHLPTIPEMGP
	HSYYRITHLPTIPE.GP
Retrocopy	HSYYRITHLPTIPETGP

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

RetrogeneDB ID:

retro_vpac_351