RetrogeneDB ID: retro_cfam_1298

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:1549826..1551204(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000006643
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMMR
• Ensembl ID: ENSCAFG00000017192
• Aliases: None
• Description: hyaluronan-mediated motility receptor (RHAMM) [Source:HGNC Symbol;Acc:5012]

Sequence

>retro_cfam_1298
ATGTCTTTTCCTAAGGCGCCCCTGAAACGATTCAATGACCCTTCCGGTTGTGCACCGTCTCCAGGTGCTTATGATGTTAA
AACTTCAGAAGTATTAAAAGGACCAGTATCATTTCAGAAATCACAAAGATTTAAAAAACAAAGAGTCTCAACAAAATCTT
AATGTTGACAGAGATACTACCTTGCCTGCTTCAGCAAGAAAAGTTAAGACTTTGGGATTAAAGAAGGAATCTCAAAAGAA
TGATAAAGATTTGAAGATACCAGAAAAAGAGATTCGTGTTCTTGTGCAAGAACATGGTGCTCAGGACAAGCAGATCCAAG
ATCTGGAAGCTGAGTTGGAGAAGGTGGAGGCCAAGCTAAATGCTGCAGTCAGGGAGAAAACATCTCTCTCCGCAAGTAAT
GCTTCACTAGAAAAACAGCTTATTGAGTTAACTAGATCTAATGAGCTACTTAAATCAAAGTTTTCTGAAGATAATAACCA
GAAGACTATGAGAATTCTAAGCCTTGAGTTAATGAAACTTAGAAATAAAGGAGAAACAAAGATGAGGAATATGATGGCTA
AACAGGAAGGCATGGAAGTGAAGCTGCAGGTCACTCAGAAGAATCTGGAGGAGTCTCGGGGAAAATAGCACAACTTGAGG
GGAAACTTGTTTCAATAGAGAAGGAAAAGACTGATGAAAAATCTGAAACAGAAAAACTCTTAGAATACATCGAAGAAATT
AGTTGTGCATCAGATCAAGTGGAGAAATACAAGCTAGATATTGCCCAATTAGAAGAAAATTTGAAAGAGAAGAATGAAGT
TGTAAGCCTTAAGCAGTCTCTTGAGGAAAATGTTGTTTTACTTTCTAAACAAGTAGAAGACCTGAATGCTAAGTGTCAGC
TACTCGAAAAAGAAAAAGAAGACCTTGTCAACAGGGATAGAGTACGGGATGAAACTCTAAAGTCTGAAATGCAAAACTTA
AAGGAGAATCTTATTCTTGAAAAACAGGAACATGAAAAACTACGACAAAAAGAATTACAGACTGATTCACTTCTGCAACA
AGAAAAGGAACTGTCCTCCAGTCTTCAACAGAAGCTACGTTCCTTTCAAGAGGAAATGATGAAAGAGAGGAATCTCTTTG
AGGAAGAATTAAAGCAAGCACTGGATGAGCTTAGATAAATTACAGCAAAAAGAGGAACAAGCTGAAAGGCTAGTCAGACA
GTTGGAAGAAAAAACAAAATCTCGAGCTGCAGAACTGAAATTCCTAGAAGAAAAGCTGAAAGGGAAAGAAGCTGAACTGG
AAGAAAGTAATGCTGCTCACAGTCAAGCCACTCTGCTTTTGCAGGAGAGCTATCATAGTATAGTGCAAAGCCTTGGAGAT
GCTACTGCTCAATTTGAA

Alignment

ORF - retro_cfam_1298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.32 %
• Parental protein coverage: 57.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSFPKAPLKRFNDPSGCAPSPGAYD-VKTSEVLKGPVSFQKSQRFKKQKESQQNLNVDRDTTLPASARKV
          MSFPKAPLKRFNDPSGCAPSPGAYD..K.....K....F.......K.KESQQNLNVDRDTTLPASARKV
Retrocopy MSFPKAPLKRFNDPSGCAPSPGAYD>LKLQKY*KDQYHF-RNHKDLKNKESQQNLNVDRDTTLPASARKV

Parental  KTLGLKKESQKNDKDLKILEKEIRVLVQERGAQDKQIQDLEAELEKVEAKLNAAVREKTSLSASNASLEK
          KTLGLKKESQKNDKDLKI.EKEIRVLVQE.GAQDKQIQDLEAELEKVEAKLNAAVREKTSLSASNASLEK
Retrocopy KTLGLKKESQKNDKDLKIPEKEIRVLVQEHGAQDKQIQDLEAELEKVEAKLNAAVREKTSLSASNASLEK

Parental  QLIELTRSNELLKSKFSEDNNQKTMRILSLELMKLRNKRETKMRNMMAKQEGMEVKLQVTQKNLEESQ-G
          QLIELTRSNELLKSKFSEDNNQKTMRILSLELMKLRNK.ETKMRNMMAKQEGMEVKLQVTQKNLEES..G
Retrocopy QLIELTRSNELLKSKFSEDNNQKTMRILSLELMKLRNKGETKMRNMMAKQEGMEVKLQVTQKNLEESR<G

Parental  KIAQLEGKLVSIEKEKTDEKSETEKLLEYIEEISCASDQVEKYKLDIAQLEENLKEKNHEVVSLKQSLEE
          KIAQLEGKLVSIEKEKTDEKSETEKLLEYIEEISCASDQVEKYKLDIAQLEENLKEKN.EVVSLKQSLEE
Retrocopy KIAQLEGKLVSIEKEKTDEKSETEKLLEYIEEISCASDQVEKYKLDIAQLEENLKEKN-EVVSLKQSLEE

Parental  NVVLLSKQVEDLNAKCQLLEKEKEDLVNRDRVRDETLNSEMQNLKENLILEKQEHEKLRQKELQTDSLLQ
          NVVLLSKQVEDLNAKCQLLEKEKEDLVNRDRVRDETL.SEMQNLKENLILEKQEHEKLRQKELQTDSLLQ
Retrocopy NVVLLSKQVEDLNAKCQLLEKEKEDLVNRDRVRDETLKSEMQNLKENLILEKQEHEKLRQKELQTDSLLQ

Parental  QEKELSSSLQQKLCSFQEEMMKERNLFEEELKQALDE-LDKLQQKEEQAERLVRQLEEETKSRAEELKLL
          QEKELSSSLQQKL.SFQEEMMKERNLFEEELKQALDE.LDKLQQKEEQAERLVRQLEE.TKSRA.ELK.L
Retrocopy QEKELSSSLQQKLRSFQEEMMKERNLFEEELKQALDE>LDKLQQKEEQAERLVRQLEEKTKSRAAELKFL

Parental  EEKLKGKEAELEESNAAHSQATLLLQESYHSIVQSLGDATAQFE
          EEKLKGKEAELEESNAAHSQATLLLQESYHSIVQSLGDATAQFE
Retrocopy EEKLKGKEAELEESNAAHSQATLLLQESYHSIVQSLGDATAQFE

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	0.08 RPM	8.40 RPM
SRP017611_brain	0.24 RPM	5.08 RPM
SRP017611_kidney	0.20 RPM	6.67 RPM
SRP017611_liver	0.00 RPM	1.96 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1298 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1298 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1298 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017192	1 retrocopy	retro_cfam_1298 ,
Callithrix jacchus	ENSCJAG00000015371	1 retrocopy	retro_cjac_3328,
Myotis lucifugus	ENSMLUG00000001674	1 retrocopy	retro_mluc_801,