RetrogeneDB - Retrocopy retro_itri

                        
>retro_itri_243
GTGAGCCATTGTTGACACAATTCCTCTGATGAAAAAAGCCTTTTTAACAATGGGCCCCCTCGAACTACAGGAGATTCCTG

GCATCAGCCCTCCCTCTTCCGCCATGATTCTGTGGACTCTGGTGTCTCTAAGGGAACATATGCTGGAATCACAGGGAACC

TATCTGGTTGGCATAGTTCTTCCTGAGGTCATGATGGCATGAACCAGCGTAGAGGAGGTGGCACAGGGAACCATCAACAC

TGGAATGGCAGTTTTCATTCCGGAAAGGCTGTGCCTTTCAAGAAAAGCCACCTACAGAGATTAGGGAAGAAAAGAAAGAA

GACAAAGTAGAAAAGTTGCAGTTTGAAGAGGAAGACTTTCCTTCTTTGAATCCAGAAGCTGGCAAACAGAATCAGCCATG

CAGATCTATTGAGACCCCTTCTGGAGTGTGGGAAAACCCACCTAGTGCCAATCAACCCTCCAAGATTCTAGTTATCAAAA

AAGTTTCCAAAGAGGATCCTGCTGCTGTCTTCTCTGCTGCATTCACCTCACCAGGATCTCACATGCAAATGGGAACAAAT

CATCAACTATGGTTCCAAGTGTCTATAAGAACTTGGTTCCTAAGCCTGCACCACCTCTTTCCAAGCCCAATGCATGGAAA

TCTAGCAAAATGGAACACAAATCAGGATCTCTTTCCTCTGACCCGGAGTCATTTACCAATCCAATTTCTGTTACCAAACC

AGTGGTACTGGCTGGTGGTGCAGTTCTCAGCTCTCCCAAAGAGAGTCCCTCCAGCATTACCCCTCCAATTGAGATCAGCT

CCTCTCCTCTAAGTTGACCAGCCAAACCACTGACAGGAAGAGTGAATTCCTAAAGACTCTGAAGGATGACTGAAATGGAG

ACTTTGCAGAGAACAGAGACTGTGACAAGCTGGAGGATTTGGAGGACAACAGCACACCTGAACCAAAGGAAAATGGGGAG

GAAGGCTGTCTTCAGAATGGTCTC

ORF - retro_itri_243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	86.09 %
Parental protein coverage:	71.71 %
Number of stop codons detected:	3
Number of frameshifts detected:	4

Retrocopy - Parental Gene Alignment:

                                ParentalVSRRRHNSSD--GFFNNGPLRTTGDSWHQPSLFRHDSVDSGVSKGTYAGITGNLSGWHSSSRGHDGINQR
VS...HNSSD....FNNGP.RTTGDSWHQPSLFRHDSVDSGVSKGTYAGITGNLSGWHSSS.GHDG.NQR
RetrocopyVSHC*HNSSDEKSLFNNGPPRTTGDSWHQPSLFRHDSVDSGVSKGTYAGITGNLSGWHSSS*GHDGMNQR
ParentalSGGGTGNHRHWNGSFHS-RKGCAFQEKPPTEIREEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRPIGT
.GGGTGNH.HWNGSFHS.RKGCAFQEKPPTEIREEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCR.I.T
RetrocopyRGGGTGNHQHWNGSFHS<RKGCAFQEKPPTEIREEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRSIET
ParentalPSGVWENPPSAKQPSKMLVIKKVSKEDPAAAFSAAFTSPGSH-HANGNKSSTMVPSVYKNLVPKPAPPPS
PSGVWENPPSA.QPSK.LVIKKVSKEDPAA.FSAAFTSPGSH.HANGNKSSTMVPSVYKNLVPKPAPP.S
RetrocopyPSGVWENPPSANQPSKILVIKKVSKEDPAAVFSAAFTSPGSH<HANGNKSSTMVPSVYKNLVPKPAPPLS
ParentalKPNAWKSSRMEHKSGSLSSSRESSFTNPISVTKPVVLAGGTVLSSP-KESPSSITPPIEISSSRL-TKLT
KPNAWKSS.MEHKSGSLSS..ES.FTNPISVTKPVVLAGG.VLSSP.K..P.....P....S..L..KLT
RetrocopyKPNAWKSSKMEHKSGSLSSDPES-FTNPISVTKPVVLAGGAVLSSP>KRVPPAL--PLQLRSAPL>SKLT
ParentalRRTTDRKSEFLKTLKDDRNGDFAENRDCDKLEDLLQLEDNSTPEPKENGEEGCLQNGL
..TTDRKSEFLKTLKDD.NGDFAENRDCDKLEDL...EDNSTPEPKENGEEGCLQNGL
RetrocopySQTTDRKSEFLKTLKDD*NGDFAENRDCDKLEDL---EDNSTPEPKENGEEGCLQNGL

                            

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

                        

RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_243 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_243 was not experimentally validated.

Retrocopy orthology:

Ictidomys tridecemlineatus 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010454	1 retrocopy	retro_chof_53,
Microcebus murinus	ENSMICG00000008449	1 retrocopy	retro_mmur_164,
Myotis lucifugus	ENSMLUG00000012432	2 retrocopies	retro_mluc_211, retro_mluc_834,
Mus musculus	ENSMUSG00000034042	2 retrocopies	retro_mmus_1391, retro_mmus_405,
Oryctolagus cuniculus	ENSOCUG00000017939	1 retrocopy	retro_ocun_427,
Otolemur garnettii	ENSOGAG00000004134	1 retrocopy	retro_ogar_1859,
Ochotona princeps	ENSOPRG00000001584	1 retrocopy	retro_opri_928,
Rattus norvegicus	ENSRNOG00000037595	1 retrocopy	retro_rnor_390,
Ictidomys tridecemlineatus	ENSSTOG00000003057	1 retrocopy	retro_itri_1678,
Ictidomys tridecemlineatus	ENSSTOG00000013491	1 retrocopy	retro_itri_243 ,

	RetrogeneDB ID:	retro_itri_243
Retrocopy location	Organism:	*Squirrel (Ictidomys tridecemlineatus)*
	Coordinates:	JH393281.1:16715967..16716951(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	GPBP1L1
	Ensembl ID:	ENSSTOG00000013491
	Aliases:	None
	Description:	GC-rich promoter binding protein 1-like 1 [Source:HGNC Symbol;Acc:28843]

Parental	VSRRRHNSSD--GFFNNGPLRTTGDSWHQPSLFRHDSVDSGVSKGTYAGITGNLSGWHSSSRGHDGINQR
	VS...HNSSD....FNNGP.RTTGDSWHQPSLFRHDSVDSGVSKGTYAGITGNLSGWHSSS.GHDG.NQR
Retrocopy	VSHCHNSSDEKSLFNNGPPRTTGDSWHQPSLFRHDSVDSGVSKGTYAGITGNLSGWHSSSGHDGMNQR

Parental	SGGGTGNHRHWNGSFHS-RKGCAFQEKPPTEIREEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRPIGT
	.GGGTGNH.HWNGSFHS.RKGCAFQEKPPTEIREEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCR.I.T
Retrocopy	RGGGTGNHQHWNGSFHS<RKGCAFQEKPPTEIREEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRSIET

Parental	PSGVWENPPSAKQPSKMLVIKKVSKEDPAAAFSAAFTSPGSH-HANGNKSSTMVPSVYKNLVPKPAPPPS
	PSGVWENPPSA.QPSK.LVIKKVSKEDPAA.FSAAFTSPGSH.HANGNKSSTMVPSVYKNLVPKPAPP.S
Retrocopy	PSGVWENPPSANQPSKILVIKKVSKEDPAAVFSAAFTSPGSH<HANGNKSSTMVPSVYKNLVPKPAPPLS

Parental	KPNAWKSSRMEHKSGSLSSSRESSFTNPISVTKPVVLAGGTVLSSP-KESPSSITPPIEISSSRL-TKLT
	KPNAWKSS.MEHKSGSLSS..ES.FTNPISVTKPVVLAGG.VLSSP.K..P.....P....S..L..KLT
Retrocopy	KPNAWKSSKMEHKSGSLSSDPES-FTNPISVTKPVVLAGGAVLSSP>KRVPPAL--PLQLRSAPL>SKLT

Parental	RRTTDRKSEFLKTLKDDRNGDFAENRDCDKLEDLLQLEDNSTPEPKENGEEGCLQNGL
	..TTDRKSEFLKTLKDD.NGDFAENRDCDKLEDL...EDNSTPEPKENGEEGCLQNGL
Retrocopy	SQTTDRKSEFLKTLKDD*NGDFAENRDCDKLEDL---EDNSTPEPKENGEEGCLQNGL

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

RetrogeneDB ID:

retro_itri_243