RetrogeneDB ID: retro_rnor_1089

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:15688722..15689625(+)
• Located in intron of: ENSRNOG00000005883

Retrocopy information

• Ensembl ID: ENSRNOG00000005869
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tcea1
• Ensembl ID: ENSRNOG00000022323
• Aliases: None
• Description: Transcription elongation factor A protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q4KLL0]

Sequence

>retro_rnor_1089
ATGGAGGACGAGGTGGTTCGCATTGCCAAGAAGATGGACAAAATGGTGCAGAAAAAGAACGCGGCCGGTGCATTGGATTT
GCTGAAAGAGCTTAAGAATATTCCCATGACCCTGGAATTATTACAGTCCACGAGAATTGGAATGTCTGTCAATGCTATTC
GCAAGCAGAGTACAGATGAAGAAGTCACATCTCTAGCCAAATCACTCATCAAATCCTGGAAAAAATTACTAGATGGACCA
TCAACTGATAAAGACTCTGAAGAAAAGAAAAAAGAACCTGCAATTTCATCACAGAATAGCCCTGAAGCAAGAGAAGAAAG
TAGTTCTAGCAGCCATGTAAGCAGCAGAAAGGATGAGACAAATGCTCGAGATACTTATGTTTCATCTTTTCCTCGGGCAC
CAAGCACTTCTGATTCTGTGCGGCTCAAGTGTAGGGAGATGCTTGCCGCAGCTCTCCGGACAGGAGATGATTATGTTGCT
ATTGGAGCTGATGAGGAAGAACTGGGATCTCAGATTGAGGAAGCTATATATCAAGAAATAAGGAATACAGACATGAAATA
CAAAAACAGAGTACGAAGTAGGATATCAAATCTTAAAGATGCAAAGAATCCAAATTTAAGGAAAAATGTGCTGTGTGGGA
ATATTCCTCCTGACCTGTTTGCTAGAATGACAGCAGAGGAAATGGCTAGTGATGAGCTCAAAGAGATGAGGAAAAACCTG
ACCAAAGAAGCCATCAGGGAGCATCAGATGGCCAAGACTGGTGGGACCCAGACTGACTTGTTCACTTGTGGCAAATGTAA
AAAGAAGAACTGCACTTACACACAGGTGCAAACTCGTAGTGCTGATGAACCAATGACAACTTTTGTTGTATGTAATGAAT
GTGGAAATCGGTGGAAGTTCTGT

Alignment

ORF - retro_rnor_1089 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDEVVRIAKKMDKMVQKKNAAGALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLI
          MEDEVVRIAKKMDKMVQKKNAAGALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLI
Retrocopy MEDEVVRIAKKMDKMVQKKNAAGALDLLKELKNIPMTLELLQSTRIGMSVNAIRKQSTDEEVTSLAKSLI

Parental  KSWKKLLDGPSTDKDSEEKKKEPAISSQNSPEAREESSSSSHVSSRKDETNARDTYVSSFPRAPSTSDSV
          KSWKKLLDGPSTDKDSEEKKKEPAISSQNSPEAREESSSSSHVSSRKDETNARDTYVSSFPRAPSTSDSV
Retrocopy KSWKKLLDGPSTDKDSEEKKKEPAISSQNSPEAREESSSSSHVSSRKDETNARDTYVSSFPRAPSTSDSV

Parental  RLKCREMLAAALRTGDDYVAIGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNV
          RLKCREMLAAALRTGDDYVAIGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNV
Retrocopy RLKCREMLAAALRTGDDYVAIGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNV

Parental  LCGNIPPDLFARMTAEEMASDELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRS
          LCGNIPPDLFARMTAEEMASDELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRS
Retrocopy LCGNIPPDLFARMTAEEMASDELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRS

Parental  ADEPMTTFVVCNECGNRWKFC
          ADEPMTTFVVCNECGNRWKFC
Retrocopy ADEPMTTFVVCNECGNRWKFC

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	1.29 RPM	25.02 RPM
SRP017611_kidney	0.49 RPM	33.98 RPM
SRP017611_liver	0.61 RPM	14.66 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

2 EST(s) were mapped to retro_rnor_1089 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CB737358	15688847	15689265	98.8	410	5	405
CF112180	15689054	15689269	100	215	0	215

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1089 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1089 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001247	1 retrocopy	retro_chof_458,
Callithrix jacchus	ENSCJAG00000014407	1 retrocopy	retro_cjac_2095,
Dasypus novemcinctus	ENSDNOG00000013799	4 retrocopies	retro_dnov_1315, retro_dnov_1853, retro_dnov_839, retro_dnov_952,
Erinaceus europaeus	ENSEEUG00000009220	1 retrocopy	retro_eeur_73,
Homo sapiens	ENSG00000187735	4 retrocopies	retro_hsap_2634, retro_hsap_4159, retro_hsap_4200, retro_hsap_4243,
Gorilla gorilla	ENSGGOG00000023652	3 retrocopies	retro_ggor_2794, retro_ggor_2814, retro_ggor_2844,
Macaca mulatta	ENSMMUG00000016022	1 retrocopy	retro_mmul_1146,
Mus musculus	ENSMUSG00000033813	2 retrocopies	retro_mmus_1369, retro_mmus_3559,
Nomascus leucogenys	ENSNLEG00000000981	3 retrocopies	retro_nleu_1028, retro_nleu_1374, retro_nleu_1384,
Oryctolagus cuniculus	ENSOCUG00000007474	3 retrocopies	retro_ocun_1382, retro_ocun_401, retro_ocun_852,
Pongo abelii	ENSPPYG00000018589	3 retrocopies	retro_pabe_3395, retro_pabe_3436, retro_pabe_3455,
Pan troglodytes	ENSPTRG00000020251	2 retrocopies	retro_ptro_2851, retro_ptro_2884,
Rattus norvegicus	ENSRNOG00000022323	1 retrocopy	retro_rnor_1089 ,
Sarcophilus harrisii	ENSSHAG00000013661	1 retrocopy	retro_shar_50,
Ictidomys tridecemlineatus	ENSSTOG00000021179	1 retrocopy	retro_itri_1745,
Tarsius syrichta	ENSTSYG00000001030	1 retrocopy	retro_tsyr_1624,