RetrogeneDB ID: retro_cfam_120

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 3:63026641..63027736(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000015116
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ACTB
• Ensembl ID: ENSCAFG00000016020
• Aliases: ACTB, ACTA1
• Description: Canis lupus familiaris actin, beta (ACTB), mRNA. [Source:RefSeq mRNA;Acc:NM_001195845]

Sequence

>retro_cfam_120
ATGAAAAGTAATATAACTGTTAATGTTTTGACTCCATTAAGAACTTTTAAAACAGTTAAATGCTCCATCGTGGGGCGCCC
CCGGCACCCCGGCGTGATGGTGGGCATGGGCCAGAAGGACTCCTACGTGGGCGATGAGGCCCAGAGCAAGAGGGGCATCC
TGACCCTGAAGTACCCCATTGAGCACGGCATCGTCACCAACTGGGACGACATGGAGAAGATCTGGCACCACACCTTCTAC
AACGAGCTGGGCGTGGCCCCCGAGGAGCACCCGGTGCTGCTGACCGAGGCCCCCCTGAACCCCAAGGCCAACCGTGAGAA
GATGACCCAGATCATGTTCGAGACTTTCAACACCCCAGCCATGTACGTGGCCATCCAGGCTGTGCTGTCCCTGTACGCCT
CTGGCCGCACCACTGGCATCGTGATGGACTCCAGTGACGGGGTCACCCACACGGTGCCCATCTATGAGGGGTACGCCCTC
CCCCATGCCATCTTGCGTCTGGACCTGGCTGGCCGGGACCTGACCGACTACCTCATGAAGATCCTCACGGAGCGTGGCTA
CAGCTTCACCACCATCGCCGAGCGGGAAATCGTGCGTGACATCAAGGAGAAGCTGTGTTATGTGGCCCTGGACTTCGAGC
AGGAGATGGCCACCGCGGCCTCCAGCTCCTCCCTGGAGAAGAGCTATGAGCTGCCCGATGGGCAGGTCATCACTATTGGC
AACGAGCGGTTCCGCTGCCCAGAGGCTCTCTTCCAGCCTTCCTTCCTGGGCATGGAATCCTGCGGCATCCATGAAACTAC
CTTCAACTCCATCATGAAGTGTGACGTTGACATCCGCAAGGACCTCTATGCCAACACAGTGCTGTCTGGTGGAACCACCA
TGTACCCTGGCATCGCTGACAGGATGCAGAAGGAGATCACTGCCCTGGCACCCAGCACAATGAAGATCAAGATCATCGCA
CCCCCTGAGCGCAAGTACTCTGTGTGGATTGGGGGCTCCATCCTGGCCTCACTGTCCACCTTCCAGCAGATGTGGATCAG
CAAGCAGGAGTACGACGAGTCCGGCCCCTCCATCGTCCACCGCAAATGCTTCTAG

Alignment

ORF - retro_cfam_120 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.83 %
• Parental protein coverage: 91.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHP
          SIVGRPRH.GVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNEL.VAPEEHP
Retrocopy SIVGRPRHPGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELGVAPEEHP

Parental  VLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALP
          VLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDS.DGVTHTVPIYEGYALP
Retrocopy VLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSSDGVTHTVPIYEGYALP

Parental  HAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYEL
          HAILRLDLAGRDLTDYLMKILTERGYSFTT.AEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYEL
Retrocopy HAILRLDLAGRDLTDYLMKILTERGYSFTTIAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYEL

Parental  PDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADR
          PDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADR
Retrocopy PDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADR

Parental  MQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF
          MQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF
Retrocopy MQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF

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	55.98 RPM	694.45 RPM
SRP017611_brain	57.80 RPM	361.16 RPM
SRP017611_kidney	43.52 RPM	277.03 RPM
SRP017611_liver	34.01 RPM	263.37 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_120 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_120 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_120 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000010147	1 retrocopy	retro_apla_2,
Canis familiaris	ENSCAFG00000016020	3 retrocopies	retro_cfam_120 , retro_cfam_260, retro_cfam_934,
Callithrix jacchus	ENSCJAG00000000008	2 retrocopies	retro_cjac_243, retro_cjac_56,
Dipodomys ordii	ENSDORG00000010079	1 retrocopy	retro_dord_11,
Equus caballus	ENSECAG00000015935	2 retrocopies	retro_ecab_271, retro_ecab_994,
Felis catus	ENSFCAG00000006788	1 retrocopy	retro_fcat_1613,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macaca mulatta	ENSMMUG00000011153	1 retrocopy	retro_mmul_135,
Otolemur garnettii	ENSOGAG00000008348	1 retrocopy	retro_ogar_2637,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pan troglodytes	ENSPTRG00000018890	27 retrocopies	retro_ptro_1042, retro_ptro_1051, retro_ptro_1076, retro_ptro_1143, retro_ptro_1272, retro_ptro_1515, retro_ptro_1756, retro_ptro_178, retro_ptro_2122, retro_ptro_2173, retro_ptro_2349, retro_ptro_2454, retro_ptro_263, retro_ptro_2805, retro_ptro_2854, retro_ptro_314, retro_ptro_3207, retro_ptro_3219, retro_ptro_3282, retro_ptro_3287, retro_ptro_3292, retro_ptro_3302, retro_ptro_3307, retro_ptro_387, retro_ptro_432, retro_ptro_53, retro_ptro_584,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,