RetrogeneDB ID: retro_cfam_227

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:21262239..21263256(-)
• Located in intron of: ENSCAFG00000014120

Retrocopy information

• Ensembl ID: ENSCAFG00000014143
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SCAMP1
• Ensembl ID: ENSCAFG00000032395
• Aliases: None
• Description: secretory carrier membrane protein 1 [Source:HGNC Symbol;Acc:10563]

Sequence

>retro_cfam_227
CAGAGCAGAGACGGCGAAAACCCCTTCATCAGGCCCGGCAAGCTTGACAACCCCTTTCAGGACCCAGCCGTGATCCAGCA
CCAACCCAGCCCGCAGTATGCCACTCTTGACGTCTACAACCCTTTTGAGACCCGGGAGCTCCCACTGGCCTATGAGCCCC
CTGCCCCTGCCCCGTTGCCTTCACCCTCGGCACCCTCCTTGCAGTCATCAAGAAAGCTCAGCCCCACAGAACCCAAGAAC
TATGGCTCCTACAGCACCCAGGCTTCAGCTGCTGCAGCCACTGCTGAGCTGCTGAAGAAGCCGGAGGAACTCAACCGGAA
GGCCGAGGAGTTGGACTGGAGGGAGCGGGAACTGCAGCATGCTGCCCTGGGGGGCACAGCTGCTCGACAGAACAATTGGC
CCCCCCTACCTTCTTTTTGCCCAGTCCAGCCCTGCTTTTTCCAGGACATCTCCATGGAGATCCCCCAAGAATTTCAGAAG
ACCGTATCTACCATGTACTACCTCTGGATGTGCAGCACACTGGCCCTTCTCCTGAATTTTCTTGCCTGCCTGGCCAGTTT
CTGTGTGGAGACCAGCAATGGCTCAGGCTTTGGGCTCTCTATCCTCTGGGTCCTCCTTTTCACTCCCTGCTCCTTTGTGT
GCTGGTACCGCCCCATGTATAAGGCCTTCCGGAGTAACAGTTCATTCAATTTCTTTGTTTTCTTCTTCATTTTCTTCGTC
CAGGATGTGCTTTTTGTCCTCCAGGCCATTGGCATCCCAGGTTGGGGGTTCAGTGGCTGGATCTCTGCTCTGGTGGTGCT
GAAGACCAACACAGCTGTAGCTGTGCTCATGCTCCTGGTTGCCCTGCTCTTCACTGGCATAGCTGTGCTGGGAATTGTGA
TGCTAAAGCGGATCCACTCCTTGTACCGCCGCACAAGTGTCAGCTTTCAGAAAGCCCAGCAAGAATTTGCTGCTGGTGTC
TCTCCTCAACCCCGCGGTGCGAACTGCTGCTGCCAACGCAGCCGCTGGCGCTGCCGA

Alignment

ORF - retro_cfam_227 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.6 %
• Parental protein coverage: 77.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPPGTVKMPNVPSTQPAI-MKPTE--EHPAYTQIAKEHALAQAELLKRQEELERKAAELDRREREMQNLS
          P.P.....P..PS.Q......PTE......Y...A...A.A.AELLK..EEL.RKA.ELD.RERE.Q...
Retrocopy PAPAPLPSPSAPSLQSSRKLSPTEPKNYGSYSTQASA-AAATAELLKKPEELNRKAEELDWRERELQHAA

Parental  QHG---RKNNWPPLPGNFPVGPCFYQDFSVDIPVEFQKTVKIMYYLWMFHAVTLFLNIFGCLAWFCVDPT
          ..G...R.NNWPPLP...PV.PCF.QD.S..IP.EFQKTV..MYYLWM.....L.LN...CLA.FCV...
Retrocopy LGGTAARQNNWPPLPSFCPVQPCFFQDISMEIPQEFQKTVSTMYYLWMCSTLALLLNFLACLASFCVETS

Parental  RGVDFGLSILWFLLFTPCSFVCWYRPLYGAFRSDSSFRFFVFFFVYICQFAVHVLQAAGFHNWGNCGWIS
          .G..FGLSILW.LLFTPCSFVCWYRP.Y.AFRS.SSF.FFVFFF....Q....VLQA.G...WG..GWIS
Retrocopy NGSGFGLSILWVLLFTPCSFVCWYRPMYKAFRSNSSFNFFVFFFIFFVQDVLFVLQAIGIPGWGFSGWIS

Parental  SLTGLNQSIPVGIMMIIIAALFTASAVISLVMFKKVHGLYRTTGASFEKAQQEFATGV
          .L..L.....V...M...A.LFT..AV...VM.K..H.LYR.T..SF.KAQQEFA.GV
Retrocopy ALVVLKTNTAVAVLMLLVALLFTGIAVLGIVMLKRIHSLYRRTSVSFQKAQQEFAAGV

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	6.01 RPM	123.77 RPM
SRP017611_brain	5.00 RPM	122.18 RPM
SRP017611_kidney	4.09 RPM	92.58 RPM
SRP017611_liver	2.54 RPM	8.12 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_227 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_227 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_227 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032395	1 retrocopy	retro_cfam_227 ,
Cavia porcellus	ENSCPOG00000008868	1 retrocopy	retro_cpor_174,
Homo sapiens	ENSG00000085365	1 retrocopy	retro_hsap_189,
Gorilla gorilla	ENSGGOG00000015191	1 retrocopy	retro_ggor_269,
Macaca mulatta	ENSMMUG00000016398	1 retrocopy	retro_mmul_396,
Monodelphis domestica	ENSMODG00000019731	1 retrocopy	retro_mdom_964,
Nomascus leucogenys	ENSNLEG00000012775	1 retrocopy	retro_nleu_1000,
Tarsius syrichta	ENSTSYG00000014113	1 retrocopy	retro_tsyr_1676,