RetrogeneDB ID: retro_cfam_1300

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:3551966..3552875(-)
• Located in intron of: ENSCAFG00000006732

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SMARCE1
• Ensembl ID: ENSCAFG00000016025
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109]

Sequence

>retro_cfam_1300
ATGCCCAGCACACCAGGGTTTGTGGGATACAATCCATACAGTCATCTCGCCTACAGGCTAGGAGGGAACCCCGGGCACCA
ACAGCTGGGGCACGGCATCCTCTGGTATTACGATTCCAAAACCCCCAAAGCCACTGATAAGCCTCTGATGCCCTACATGA
GGTACAGCAGAAAGGTCTGGGACCCAATAAAAGCTTCCAACCCTGACCTAAAGTTGTGGGAGATTGGCAAGATTATTGGT
GGCATGTGGCGAGATCTCACTGATGAAGAAAAACAAGAATATTTAAACGAATACGAAGCAGAAAAGATAGAGTACAAGGA
ATCTATGAAGGTCTAGCATAATTCCCTCGCATCCCTTACTTACATAAATTCGAAAAGTCGTGCAAAAGCTGCTTTAGAGG
AAGAAAGTCGACAGAGACAGTTTCGCATGGAGAAAGGAGAACCTTACCTGAGTATTCAGCCTGCTGAAGATCCAGATGAT
TATGATGATGGCTTTTCAATGAAGCCTACAGCCACTGCCCATTTCCAGAGAAACCACTGCCTCATCAGTGAAACCCTTAG
TGAGAGTGTGGTGCCAGACGTTCGGTCAGTTGTCACAACAGCTAGAATGCAGGTCCTCAAACGACAGGTCCAGTCCTTAA
TGGTTCATCAGCGAAAACTAGAAGCTGAACTTCTTCAGATAGAGGAGCGACACCAGGAAAAGAAGAGGAAGTTCCTAGAA
AGCACAGATTCATTTAACAATGAACTTAAAAGGTTGTGGGGTTTGAAAGTAGAAGTGGATACGGAAAAGGTTGCCGCTGA
AATTGCACAGGCCGAAGAGCAGGCCCGCAAAAGGCAAGAGGAGAGGGAGAGAGAAGCAGCAGAGCAAGCTGAACGTAGTC
AGAGCAGCACGGTTCCCGAGGAAGAGCCA

Alignment

ORF - retro_cfam_1300 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.58 %
• Parental protein coverage: 77.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPSTPGFVGYNPYSHLAYNNYRLGGN-PGTNSRVTASSGITIPKPPKP-PDKPLMPYMRYSRKVWDQVKA
          MPSTPGFVGYNPYSHLAY...RLGGN.PGTNS..TASSGITIPKPPKP..DKPLMPYMRYSRKVWD..KA
Retrocopy MPSTPGFVGYNPYSHLAY---RLGGN>PGTNSWGTASSGITIPKPPKP<TDKPLMPYMRYSRKVWDPIKA

Parental  SNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYLAYINAKSRAEAALEEE
          SNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYEAEKIEY.ESMK..HNS.A.L.YIN.KSRA.AALEEE
Retrocopy SNPDLKLWEIGKIIGGMWRDLTDEEKQEYLNEYEAEKIEYKESMKV*HNSLASLTYINSKSRAKAALEEE

Parental  SRQRQSRMEKGEPYMSIQPAEDPDDYDDGFSMKHTATARFQRNHRLISEILSESVVPDVRSVVTTARMQV
          SRQRQ.RMEKGEPY.SIQPAEDPDDYDDGFSMK.TATA.FQRNH.LISE.LSESVVPDVRSVVTTARMQV
Retrocopy SRQRQFRMEKGEPYLSIQPAEDPDDYDDGFSMKPTATAHFQRNHCLISETLSESVVPDVRSVVTTARMQV

Parental  LKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTDSFNNELKRLCGLKVEVDMEKIAAEIAQAEEQA
          LKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTDSFNNELKRL.GLKVEVD.EK.AAEIAQAEEQA
Retrocopy LKRQVQSLMVHQRKLEAELLQIEERHQEKKRKFLESTDSFNNELKRLWGLKVEVDTEKVAAEIAQAEEQA

Parental  RKRQEEREKEAAEQAERSQSSMVPEEEP
          RKRQEERE.EAAEQAERSQSS.VPEEEP
Retrocopy RKRQEEREREAAEQAERSQSSTVPEEEP

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	0.00 RPM	32.51 RPM
SRP017611_brain	0.00 RPM	11.04 RPM
SRP017611_kidney	0.00 RPM	21.59 RPM
SRP017611_liver	0.00 RPM	7.03 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1300 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1300 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016025	8 retrocopies	retro_cfam_1057, retro_cfam_1131, retro_cfam_1134, retro_cfam_1300 , retro_cfam_1412, retro_cfam_1803, retro_cfam_2063, retro_cfam_2127,
Choloepus hoffmanni	ENSCHOG00000008727	3 retrocopies	retro_chof_1245, retro_chof_482, retro_chof_573,
Callithrix jacchus	ENSCJAG00000013573	4 retrocopies	retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Felis catus	ENSFCAG00000009646	2 retrocopies	retro_fcat_234, retro_fcat_513,
Gorilla gorilla	ENSGGOG00000011803	2 retrocopies	retro_ggor_1020, retro_ggor_931,
Macaca mulatta	ENSMMUG00000004005	3 retrocopies	retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furo	ENSMPUG00000014660	4 retrocopies	retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Oryctolagus cuniculus	ENSOCUG00000008981	1 retrocopy	retro_ocun_59,
Pongo abelii	ENSPPYG00000008456	4 retrocopies	retro_pabe_2973, retro_pabe_3251, retro_pabe_794, retro_pabe_994,
Rattus norvegicus	ENSRNOG00000010676	7 retrocopies	retro_rnor_1278, retro_rnor_1311, retro_rnor_1456, retro_rnor_1507, retro_rnor_1599, retro_rnor_2383, retro_rnor_2593,
Tursiops truncatus	ENSTTRG00000013885	1 retrocopy	retro_ttru_1217,