RetrogeneDB ID: retro_mmus_1369

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:90882614..90883517(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000067869
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tcea1
• Ensembl ID: ENSMUSG00000033813
• Aliases: Tcea1, S-II
• Description: transcription elongation factor A (SII) 1 [Source:MGI Symbol;Acc:MGI:1196624]

Sequence

>retro_mmus_1369
ATGGAGGACGAGGTGGTTCGCATTGCCAAGAAGATGGACAAAATGGTGCAGAAAAAGAATGCGGCTGGCGCATTGGATTT
GCTGAAAGAGCTTAAGAATATTCCCATGACCCTAGAATTGCTACAGTCCACAAGAATTGGAATGTCTGTCAATGCTCTTC
GCAAGCAGAGCACAGATGAAGAAGTCACCTCTCTAGCCAAGTCTCTCATCAAATCCTGGAAAAAATTATTAGATGGACCA
TCAACTGATAAAGACCCTGAAGAAAAGAAAAAAGAGCCTGCAATTTCATCACAGAATAGCCCTGAAGCAAGAGAAGAAAG
TAGTTCCAGCAGCAATGTAAGCAGCAGAAAGGATGAGACAAATGCTCGAGATACATATGTTTCATCTTTTCCTCGGGCAC
CAAGCACTTCTGATTCTGTGTGATTAAAATGTAGGGAGATGCTTGCTGCAGCTCTTCGGACAGGAGATGATTATGTTGCA
ATTGGAGCTGATGAAGAAGAACTGGGATCTCAGATTGAGGAAGCTATATATCAAGAAATAAGGAATACAGACATGAAATA
CAAAAACAGAGTACGAAGTAGGATATCAAATCTTAAAGATGCAAAGAATCCAAATTTAAGGAAAAATGTGCTGTGTGGGA
ATGTTCCTCCTGACCTATTTGCTAGAATGAAAGCAGAGGAAATGGCTAGTGATGAGCTCAAAGAGATGAGGAAAAACCTG
ACCAAAGAAGCCATCAGGGAGCATCAGATGGCCAAGACTGGTGGGACCCAGACTGACTTGTTCACTTGTGGCAAATGTAA
AAAGAAGAACTGCACTTACACACAGGTGCAAACTCGTAGTGCTGATGAACCAATGACAACATTTGTTGTATGTAATGAAT
GTGGAAATCGGTGGAAGTTCTGT

Alignment

ORF - retro_mmus_1369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDEVVRIAKKMDKMVQKKNAAGALDLLKELKNIPMTLELLQSTRIGMSVNALRKQSTDEEVTSLAKSLI
          MEDEVVRIAKKMDKMVQKKNAAGALDLLKELKNIPMTLELLQSTRIGMSVNALRKQSTDEEVTSLAKSLI
Retrocopy MEDEVVRIAKKMDKMVQKKNAAGALDLLKELKNIPMTLELLQSTRIGMSVNALRKQSTDEEVTSLAKSLI

Parental  KSWKKLLDGPSTDKDPEEKKKEPAISSQNSPEAREESSSSSNVSSRKDETNARDTYVSSFPRAPSTSDSV
          KSWKKLLDGPSTDKDPEEKKKEPAISSQNSPEAREESSSSSNVSSRKDETNARDTYVSSFPRAPSTSDSV
Retrocopy KSWKKLLDGPSTDKDPEEKKKEPAISSQNSPEAREESSSSSNVSSRKDETNARDTYVSSFPRAPSTSDSV

Parental  RLKCREMLAAALRTGDDYVAIGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNV
          .LKCREMLAAALRTGDDYVAIGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNV
Retrocopy *LKCREMLAAALRTGDDYVAIGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNV

Parental  LCGNIPPDLFARMTAEEMASDELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRS
          LCGN.PPDLFARM.AEEMASDELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRS
Retrocopy LCGNVPPDLFARMKAEEMASDELKEMRKNLTKEAIREHQMAKTGGTQTDLFTCGKCKKKNCTYTQVQTRS

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
SRP007412_brain	0.37 RPM	10.42 RPM
SRP007412_cerebellum	1.04 RPM	7.21 RPM
SRP007412_heart	0.22 RPM	4.17 RPM
SRP007412_kidney	1.06 RPM	9.03 RPM
SRP007412_liver	0.44 RPM	7.67 RPM
SRP007412_testis	0.96 RPM	8.78 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1369 was not detected

EST

3 EST(s) were mapped to retro_mmus_1369 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AV119670	90882596	90882873	96.4	267	10	257
AV578435	90882903	90883034	100	131	0	131
BY021910	90882623	90882895	98.6	268	2	263

TSS

No TSS is located nearby retro_mmus_1369 retrocopy 5' end.

Lab

retro_mmus_1369 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1369 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,