RetrogeneDB ID: retro_cfam_1615

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 37:2798669..2799526(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000010125
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TSG101
• Ensembl ID: ENSCAFG00000009279
• Aliases: None
• Description: tumor susceptibility gene 101 [Source:HGNC Symbol;Acc:15971]

Sequence

>retro_cfam_1615
GGAAAGCATGCTGATGCAAATGAGAAGATATATCTTCCTTCTCTACATAAATGGAAACACCACAGCCAGACTTGTTTATT
CAGGTCATGATTGTGGTGTTTGGAGATGAACCTCCAGTCTTCTCTCGTCTCACTATTTTGGCATCTTATCCACTATACCA
GGCAAAGGGGCAACCCAATACTTCCTATATGCCAAGTATGCCAAGTGGAATATCTGCATATCCATCCAGATATCCTCCCA
ACCCCAGTGGTTATCCAGGCTGTCCTTACCCACCTCTGGTCAGTATCCTGCCACAGGTTCTCAATACCCTTCCCAGCTCC
CGTGGCCACTGTCAGTCCCAATAGGGATGACACCATTGGTGAGGTCACCATTCGAGCCTCTCTCATCTCAGTGGTTAGTG
ACAAGCTGAGATGGCAGAGGAAGGAGGAAATGGATCATGCCCAGGCAGGGCTCAATGCCTTGAAACAAACAGAGGAAGAC
CTGAAGAAAGGTGATCAGAAACTGGAAGAGATGGTTACCCGTTTAGATCAAGAAGTAGCTGAGGTCGATAAAAACATAGA
ACTTTTGAGAAAGAAGAATGAAGAACTCAGTTCTGTTCTGGAGAAAATCAGTCTGAAAACAATGACACTGATGAAGTTAT
CATTCCGACAGTCCCACTATACAAACAGATCCTAAATCTGTATGCAGAGGAAAATGCTATTGAAGACACTATCTTTTACC
TGGGAGAAGCCTTGAGGTGGGGAGTAATAGGTTTGGGTGTCTTCCTGAAGCATGTACATCTTCTGTCCCATAAACAGTTC
CAGCTGGGGGCACTAATGCAAAAAGCAAGAAAGACTGCTAATCTCTGTGACCTCTAC

Alignment

ORF - retro_cfam_1615 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.42 %
• Parental protein coverage: 74.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GKHVDANGKIYLPYLHEWKH-PQSDLLGLIQVMIVVFGDEPPVFSRPTISASYPPYQATGPPNTSYMPSM
          GKH.DAN.KIYLP.LH.WKH.PQ.DL...IQVMIVVFGDEPPVFSR.TI.ASYP.YQA.G.PNTSYMPSM
Retrocopy GKHADANEKIYLPSLHKWKH<PQPDLF--IQVMIVVFGDEPPVFSRLTILASYPLYQAKGQPNTSYMPSM

Parental  PSGISAYPSGYPPNPSGYPGCPYPP-GGQYPATTSSQYPSQ-PPVATVGPSRDGTISEDTIRASLISAVS
          PSGISAYPS.YPPNPSGYPGCPYPP..GQYPAT..SQYPSQ..PVATV.P.RD.TI.E.TIRASLIS.VS
Retrocopy PSGISAYPSRYPPNPSGYPGCPYPP<SGQYPAT-GSQYPSQ<APVATVSPNRDDTIGEVTIRASLISVVS

Parental  DKLRWRMKEEMDRAQAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLRKKDEELSSALEKM
          DKLRW..KEEMD.AQA.LNALK.TEEDLKKG.QKLEEMVTRLDQEVAEVDKNIELLRKK.EELSS.LEK.
Retrocopy DKLRWQRKEEMDHAQAGLNALKQTEEDLKKGDQKLEEMVTRLDQEVAEVDKNIELLRKKNEELSSVLEKI

Parental  -ENQSENNDIDEVIIPTAPLYKQILNLYAEENAIEDTIFYLGEALRRGVIDLDVFLKHVRLLSRKQFQLR
          ........D..EVIIPT.PLYKQILNLYAEENAIEDTIFYLGEALR.GVI.L.VFLKHV.LLS.KQFQL.
Retrocopy <QSENNDTD--EVIIPTVPLYKQILNLYAEENAIEDTIFYLGEALRWGVIGLGVFLKHVHLLSHKQFQLG

Parental  ALMQKARKTAGLSDLY
          ALMQKARKTA.L.DLY
Retrocopy ALMQKARKTANLCDLY

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.04 RPM	37.25 RPM
SRP017611_brain	0.00 RPM	32.31 RPM
SRP017611_kidney	0.00 RPM	61.08 RPM
SRP017611_liver	0.00 RPM	16.61 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1615 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1615 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1615 has 0 orthologous retrocopies within eutheria group .

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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,