RetrogeneDB - Retrocopy retro_mmus

                        
>retro_mmus_1350
CATGTTTTTAATGATGGCAGTTCCAGGGAGCTGGTGAACCTCACTGGTACAATCCCAGTGTGTTATCGAGGTAATATATA

TAATATTCCAATATGCCTGTGGCTGCTGGACACATATATAACCCCCCCATCTGTTTTGTTAAGCCTACTAGTTCAATGAC

TATTAAAACAGGAAAGCATGTGGATGCAAATGGGAAAATCTACCTACCTTATCTACATGACTGGAAACATCCACAGTCAG

AGTTGCTGGAGCTTATTCAAATCATGATTGTGATATTTGGAGAGGAGCCTCCAGTGTTCTCCCGGCCTACTGTTTCTGCA

TCCTACCCACCATACACAGCAACAGGGCCACCAAATACCTCCTACATGCCAGGCATGCCAAGTGGAATCTCTGCATATCC

ATCTGGATACCCTCCCAACCCCAGTGGTTATCCTGGCTGTCCTTACCCACCTGCTGGCCCATACCCTGCCACAACAAGCT

CACAGTACCCTTCCCAGCCTCCTGTGACCACTGTTGGTCCCAGCAGAGATGGCACAATCAGTGAGGACACTATCCAAGCA

TCTCTCATCTCAGCAGTCAGTGACAAACTGAGATGGTGGATGAAGGAGGAAATGGATGGTGCCCAGGCAGAGCTTAATGC

CTTGAAACGAACAGAGGAAGATCTGAAAAAAGGCCACCAGAAACTGGAAGAGATGGTCACCCGCTTAGATCAAGAAGTAG

CTGAAGTTGATAAAAACATAGAACTTTTGAAAAAGAAGGATGAAGAACTAAGTCCTGCTCTGGAGAAAATGGAAAATCAA

TCTGAAAATAATGATATTGATGAAGTTATCATTCCCACAGCCCCACTGTATAAACAGATTCTAAATCTGTACGCAGAGGA

AAATGCTATTGAAGACACTATCTTTTACCTTGGAGAAGCTTTGCGGTGGGGAGTAATAGACCTGGATGTGTTCCTGAAGC

ACTTCAGCCTCCTGTCCCTTAAACAGTTCCAGCTAAGGGCACTAATACAAAAGGCAAGGAAGACTGCGGGCCTTAGTGAC

CTCTAC

ORF - retro_mmus_1350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	95.73 %
Parental protein coverage:	89.51 %
Number of stop codons detected:	0
Number of frameshifts detected:	1

Retrocopy - Parental Gene Alignment:

                                ParentalYVFNDGSSRELVNLTGTIPVRYRGNIYNIPICLWLLDTYPYNPP-ICFVKPTSSMTIKTGKHVDANGKIY
.VFNDGSSRELVNLTGTIPV.YRGNIYNIPICLWLLDTY...PP.ICFVKPTSSMTIKTGKHVDANGKIY
RetrocopyHVFNDGSSRELVNLTGTIPVCYRGNIYNIPICLWLLDTY-ITPP<ICFVKPTSSMTIKTGKHVDANGKIY
ParentalLPYLHDWKHPRSELLELIQIMIVIFGEEPPVFSRPTVSASYPPYTATGPPNTSYMPGMPSGISAYPSGYP
LPYLHDWKHP.SELLELIQIMIVIFGEEPPVFSRPTVSASYPPYTATGPPNTSYMPGMPSGISAYPSGYP
RetrocopyLPYLHDWKHPQSELLELIQIMIVIFGEEPPVFSRPTVSASYPPYTATGPPNTSYMPGMPSGISAYPSGYP
ParentalPNPSGYPGCPYPPAGPYPATTSSQYPSQPPVTTVGPSRDGTISEDTIRASLISAVSDKLRWRMKEEMDGA
PNPSGYPGCPYPPAGPYPATTSSQYPSQPPVTTVGPSRDGTISEDTI.ASLISAVSDKLRW.MKEEMDGA
RetrocopyPNPSGYPGCPYPPAGPYPATTSSQYPSQPPVTTVGPSRDGTISEDTIQASLISAVSDKLRWWMKEEMDGA
ParentalQAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEELSSALEKMENQSENNDIDEVII
QAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEELS.ALEKMENQSENNDIDEVII
RetrocopyQAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEELSPALEKMENQSENNDIDEVII
ParentalPTAPLYKQILNLYAEENAIEDTIFYLGEALRRGVIDLDVFLKHVRLLSRKQFQLRALMQKARKTAGLSDL
PTAPLYKQILNLYAEENAIEDTIFYLGEALR.GVIDLDVFLKH..LLS.KQFQLRAL.QKARKTAGLSDL
RetrocopyPTAPLYKQILNLYAEENAIEDTIFYLGEALRWGVIDLDVFLKHFSLLSLKQFQLRALIQKARKTAGLSDL
ParentalY
Y
RetrocopyY

                            

                            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	0 .23 RPM	31 .63 RPM
SRP007412_cerebellum	0 .35 RPM	27 .79 RPM
SRP007412_heart	0 .25 RPM	25 .06 RPM
SRP007412_kidney	0 .31 RPM	27 .91 RPM
SRP007412_liver	0 .14 RPM	19 .33 RPM
SRP007412_testis	0 .14 RPM	15 .73 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_1350 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1350 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_1350 retrocopy 5' end.

Lab - click to see more details

retro_mmus_1350 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_mmus_1350 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013563	4 retrocopies	retro_btau_1009, retro_btau_698, retro_btau_825, retro_btau_979,
Canis familiaris	ENSCAFG00000009279	1 retrocopy	retro_cfam_1615,
Cavia porcellus	ENSCPOG00000011994	1 retrocopy	retro_cpor_1420,
Myotis lucifugus	ENSMLUG00000016353	2 retrocopies	retro_mluc_1133, retro_mluc_1713,
Mus musculus	ENSMUSG00000014402	1 retrocopy	retro_mmus_1350 ,

	RetrogeneDB ID:	retro_mmus_1350
Retrocopy location	Organism:	*Mouse (Mus musculus)*
	Coordinates:	15:62980768..62981814(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Tsg101
	Ensembl ID:	ENSMUSG00000014402
	Aliases:	Tsg101, AI255943, CC2
	Description:	tumor susceptibility gene 101 [Source:MGI Symbol;Acc:MGI:106581]

Parental	YVFNDGSSRELVNLTGTIPVRYRGNIYNIPICLWLLDTYPYNPP-ICFVKPTSSMTIKTGKHVDANGKIY
	.VFNDGSSRELVNLTGTIPV.YRGNIYNIPICLWLLDTY...PP.ICFVKPTSSMTIKTGKHVDANGKIY
Retrocopy	HVFNDGSSRELVNLTGTIPVCYRGNIYNIPICLWLLDTY-ITPP<ICFVKPTSSMTIKTGKHVDANGKIY

Parental	LPYLHDWKHPRSELLELIQIMIVIFGEEPPVFSRPTVSASYPPYTATGPPNTSYMPGMPSGISAYPSGYP
	LPYLHDWKHP.SELLELIQIMIVIFGEEPPVFSRPTVSASYPPYTATGPPNTSYMPGMPSGISAYPSGYP
Retrocopy	LPYLHDWKHPQSELLELIQIMIVIFGEEPPVFSRPTVSASYPPYTATGPPNTSYMPGMPSGISAYPSGYP

Parental	PNPSGYPGCPYPPAGPYPATTSSQYPSQPPVTTVGPSRDGTISEDTIRASLISAVSDKLRWRMKEEMDGA
	PNPSGYPGCPYPPAGPYPATTSSQYPSQPPVTTVGPSRDGTISEDTI.ASLISAVSDKLRW.MKEEMDGA
Retrocopy	PNPSGYPGCPYPPAGPYPATTSSQYPSQPPVTTVGPSRDGTISEDTIQASLISAVSDKLRWWMKEEMDGA

Parental	QAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEELSSALEKMENQSENNDIDEVII
	QAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEELS.ALEKMENQSENNDIDEVII
Retrocopy	QAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLKKKDEELSPALEKMENQSENNDIDEVII

Parental	PTAPLYKQILNLYAEENAIEDTIFYLGEALRRGVIDLDVFLKHVRLLSRKQFQLRALMQKARKTAGLSDL
	PTAPLYKQILNLYAEENAIEDTIFYLGEALR.GVIDLDVFLKH..LLS.KQFQLRAL.QKARKTAGLSDL
Retrocopy	PTAPLYKQILNLYAEENAIEDTIFYLGEALRWGVIDLDVFLKHFSLLSLKQFQLRALIQKARKTAGLSDL

Parental	Y
	Y
Retrocopy	Y

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

RetrogeneDB ID:

retro_mmus_1350