RetrogeneDB ID: retro_cpor_278

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_113:4038747..4040583(-)
• Located in intron of: ENSCPOG00000013881

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000005595
• Aliases: None
• Description: None

Sequence

>retro_cpor_278
GCAAAAAAGAAGAAGAAGAAGGGGAAGACTATCCCCCTAACCGACTTTCTGGCTGAGGATAGAGGGACTGGTGGAGGAAC
CACCTATGTTCCCAAACCAGTCAGCTGGGCTGATGAAACAGATGACCTGGAAGGAGATGTTTCAACCCCTTGGCACAGTA
ACGATGATGATGTGTATAGGGCACCTCCAATTGACCGTTCCATCCTTCCCACTGCTCCACGAGCTGCTCGGGAACCCAAT
ATCGACCGGAGCCGTCTTCCCAAATCGCCACCCTACACTGCTTTTCTAGGAAACTTGCCCTATGAAGTGACAGAAGACTC
TATTAAGGAATTCTTTAGAGGCTTAAATATCCGTGCAGTGCGTTTGCCACGTGAACCCAGCAATCCAGACAGGTTGAAAG
GTTTTGGTTATGCTGAGTTTGAGGACCTGGATTCCCTGCTCAGTGCCCTGAGTCTCAATGAAGAGTCTCTAGGTAACAGG
AGAATTCGAGTGGATGTTGCTGATCAAGCACAGGATAAAGGCCGGGATGATCGTTCTTTCTGGCGAGATAGAAATCGACA
TTCTGACAAAACAGACACAGACTGGAGGGCACGTCCTGCCACAGACAGCTTTGATGACTATCCACCAAGAAGAGGTGATG
ATAGCTTTGGCGACAAGTATCGAGATCGTTATGATCCAGACCGGTACCGTGATGGGTATCGGGATAGAGATGGCTATCGG
GATGGCCCACGCCGGGGTATGGATCGATATAAAGGCCGAGTTCGATATGATGACCGAGGCAGCAGAGACTATGATAGAGG
CTATGATTCCAGAATAGGCAGTGGCAGAAGAGCCTTTGGTAGTGGGTACCGTAGATATGATCATTACAGAGGAGGAGGAG
CCCGATATGAAGACCGGTATGACAGACGAGATGATCGACCTTGGGGCTCCAGAGATGATTACTCACGGGACGATTATAGA
CGTGATGACAGAGGTCCCCCCCAAAGACCCAAACTGAACCTAAAGCCTCGGAGTACTCCTAAGGAAGATGATTCTTCTGC
TAGTACCTCCCAGTCCAGTCGAGCAGCTTCTATCTTTGGAGGGGCAAAGCCTGTTGACACGGCTGCCAGAGAAAGAGAAG
TGGAAGAACGGCTACAGAAAGAGCAGGAGAAGCTGCAACGGCAGCTGGATGAGCCGAAACTAGAACGACGGCCTTGGGAA
AGACAGCCAAGCTGGCGAAGTGAAGAAACTCAGGAACAGGAAAGATCAAGGACAGGAAGCGAATCATCACAGACTGGAAC
CTCAGCCCCATCTGGCAGAAGTAAGTTAGACCAGGATGCCCGAAGAAGAGAGAGTGAGAAGTCTCTAGAAAATGAAACAC
TCAGTAAGGAGGAAGACTGTCACTCTCCAACTTGTAAGCCTCCCAAACCTGATCAGCCTCTAAAAGTAATGCCAGCCCCT
CCACCGAAGGAGAATGCATGGGTGAAGCGAAGTTCTAACGCTCCTGCTCGATCTCAGAGCTCAGACACAGAGCACCAATC
TCCTACAAGTGGTGGGGGGAAACTAGCTCCAGCTCAGCCTTCTGAGGAGGGACCATCAAGGAAAGATGAAAATAATGGAA
TGAGTACCCAAAAAGGCCAAACTGGGAACTCCATCCGTGGTCCAGGAGATGGAGGGAACAAAGACCTTTGGAAGGAGTCA
GATAGGAAAGATGGCAAAAAGGATCAAGACTCTAGATCTTCACCTGAGCCAAAGAAACTTGAGGAAAATCCAGCCTCCAA
GTTCAGTTCTGCAAGCAAGTATGCTGCTCTCGGCATGGATGGTGAAGATGATAATGAAGGAGAAGACTACACTGAC

Alignment

ORF - retro_cpor_278 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.05 %
• Parental protein coverage: 99.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKKKNKKGKTISLTDFLAEDGGTGGGTTYVPKPVSWADETDDLEGDVSTTWHSNDDDVYRAPPIDRSILP
          AKKK.KKGKTI.LTDFLAED.GTGGGTTYVPKPVSWADETDDLEGDVST.WHSNDDDVYRAPPIDRSILP
Retrocopy AKKKKKKGKTIPLTDFLAEDRGTGGGTTYVPKPVSWADETDDLEGDVSTPWHSNDDDVYRAPPIDRSILP

Parental  TAPRAAREPNIDRSRLPKSPPYTAFLGNLPYEVTEDSIKEFFRGLNISAVRLPREPSNPDRLKGFGYAEF
          TAPRAAREPNIDRSRLPKSPPYTAFLGNLPYEVTEDSIKEFFRGLNI.AVRLPREPSNPDRLKGFGYAEF
Retrocopy TAPRAAREPNIDRSRLPKSPPYTAFLGNLPYEVTEDSIKEFFRGLNIRAVRLPREPSNPDRLKGFGYAEF

Parental  EDLDSLLSALSLNEESLGNRRIRVDVADQAQDKDRDDRSFGRDRNRDSDKTDTDWRARPATDSFDDYPPR
          EDLDSLLSALSLNEESLGNRRIRVDVADQAQDK.RDDRSF.RDRNR.SDKTDTDWRARPATDSFDDYPPR
Retrocopy EDLDSLLSALSLNEESLGNRRIRVDVADQAQDKGRDDRSFWRDRNRHSDKTDTDWRARPATDSFDDYPPR

Parental  RGDDSFGDKYRDRYDSDRYRDGYRDRDGYRDGPRRDMDRYGGRDRYDDRGSRDYDRGYDSRIGSGRRAFG
          RGDDSFGDKYRDRYD.DRYRDGYRDRDGYRDGPRR.MDRY.GR.RYDDRGSRDYDRGYDSRIGSGRRAFG
Retrocopy RGDDSFGDKYRDRYDPDRYRDGYRDRDGYRDGPRRGMDRYKGRVRYDDRGSRDYDRGYDSRIGSGRRAFG

Parental  SGYRRDDDYRGGGDRYEDRYDRRDDRPWGSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTS
          SGYRR.D.YRGGG.RYEDRYDRRDDRPWGSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTS
Retrocopy SGYRRYDHYRGGGARYEDRYDRRDDRPWGSRDDYSRDDYRRDDRGPPQRPKLNLKPRSTPKEDDSSASTS

Parental  QSSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPRERHPSWRSEETQERERSRTGS
          QSSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRP.ER.PSWRSEETQE.ERSRTGS
Retrocopy QSSRAASIFGGAKPVDTAAREREVEERLQKEQEKLQRQLDEPKLERRPWERQPSWRSEETQEQERSRTGS

Parental  ESSQTGTSAPSGRNARRRESEKSLENETLSKEEDCHSPTSKPP--KPDQP---LKVMPAPPPKENAWVKR
          ESSQTGTSAPSGR...............L..E..........P..KP..P...LKVMPAPPPKENAWVKR
Retrocopy ESSQTGTSAPSGRSKLDQDARRRESEKSLENETLSKEEDCHSPTCKPPKPDQPLKVMPAPPPKENAWVKR

Parental  SSNPSARSQSSDTEHQSPTSGGGKLAPAQPSEEGPARKADENNGMSTQKGQTGNSIRGLGDGGNKDHWKE
          SSN..ARSQSSDTEHQSPTSGGGKLAPAQPSEEGP.RK.DENNGMSTQKGQTGNSIRG.GDGGNKD.WKE
Retrocopy SSNAPARSQSSDTEHQSPTSGGGKLAPAQPSEEGPSRK-DENNGMSTQKGQTGNSIRGPGDGGNKDLWKE

Parental  SDRKDGKKDQDSRSAPEPKKLEENPASKFSSASKYAALCMDGEDDNEGEDYTE
          SDRKDGKKDQDSRS.PEPKKLEENPASKFSSASKYAAL.MDGEDDNEGEDYT.
Retrocopy SDRKDGKKDQDSRSSPEPKKLEENPASKFSSASKYAALGMDGEDDNEGEDYTD

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
SRP017611_brain	1.44 RPM	70.40 RPM
SRP017611_kidney	1.78 RPM	93.38 RPM
SRP017611_liver	1.57 RPM	90.88 RPM
SRP040447_lung	0.28 RPM	98.49 RPM
SRP040447_skeletal_muscle	0.24 RPM	104.17 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_278 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_278 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012023	2 retrocopies	retro_amel_1107, retro_amel_559,
Canis familiaris	ENSCAFG00000007117	2 retrocopies	retro_cfam_1447, retro_cfam_936,
Choloepus hoffmanni	ENSCHOG00000001608	2 retrocopies	retro_chof_1310, retro_chof_366,
Callithrix jacchus	ENSCJAG00000018176	2 retrocopies	retro_cjac_1717, retro_cjac_2001,
Cavia porcellus	ENSCPOG00000005595	3 retrocopies	retro_cpor_278 , retro_cpor_752, retro_cpor_937,
Homo sapiens	ENSG00000063046	7 retrocopies	retro_hsap_1686, retro_hsap_2639, retro_hsap_2698, retro_hsap_3767, retro_hsap_4196, retro_hsap_4848, retro_hsap_4891,
Gorilla gorilla	ENSGGOG00000013695	5 retrocopies	retro_ggor_1233, retro_ggor_1263, retro_ggor_1882, retro_ggor_1883, retro_ggor_3024,
Loxodonta africana	ENSLAFG00000009534	1 retrocopy	retro_lafr_294,
Macropus eugenii	ENSMEUG00000012341	2 retrocopies	retro_meug_1054, retro_meug_585,
Macaca mulatta	ENSMMUG00000001062	5 retrocopies	retro_mmul_1428, retro_mmul_2384, retro_mmul_2589, retro_mmul_731, retro_mmul_783,
Mus musculus	ENSMUSG00000058655	1 retrocopy	retro_mmus_3686,
Nomascus leucogenys	ENSNLEG00000017727	3 retrocopies	retro_nleu_2371, retro_nleu_2601, retro_nleu_721,
Pongo abelii	ENSPPYG00000025848	7 retrocopies	retro_pabe_1388, retro_pabe_1560, retro_pabe_2283, retro_pabe_260, retro_pabe_3532, retro_pabe_3768, retro_pabe_506,
Rattus norvegicus	ENSRNOG00000010103	2 retrocopies	retro_rnor_2467, retro_rnor_2972,
Ictidomys tridecemlineatus	ENSSTOG00000006800	1 retrocopy	retro_itri_604,
Tupaia belangeri	ENSTBEG00000005423	2 retrocopies	retro_tbel_2363, retro_tbel_4167,
Tarsius syrichta	ENSTSYG00000012880	1 retrocopy	retro_tsyr_452,