RetrogeneDB ID: retro_btau_1592

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:105590750..105591476(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A4
• Ensembl ID: ENSBTAG00000013208
• Aliases: SLC25A4, ANT1
• Description: ADP/ATP translocase 1 [Source:UniProtKB/Swiss-Prot;Acc:P02722]

Sequence

>retro_btau_1592
GTCACGCCCATCGAGAGGGTCAAACTGCTGCTGCAGGTCCAGCATGCCAGCAAACAGATCAGTGCTGAGAAGCAGTACAA
AGGGATCATTGATTGCGTGGTGAGAATCCCCAAGGAGCAGGGCTTTCTCTCCTTCTGGAGGGGTAACCTGGCCAACGTGA
TCCGTTACTTCCCCACCCAAGCTCTCAACTTCGCCTTCAAGGACAAGTACAAGCAGATCTTCTTGGGGGGCGTGGACCGG
CATAAGCAGTTCTGGCGCTACTTTGCCGGTAACCTGGCCTCCGGTGGGGCAGCTGGGGCCACCTCCCTCTGCTTTGTCTA
CCCGCTGGACTTCGCTAGGACCAGGCTGGCTGCCGACGTGGGCAAGGGTGCCGCCCAGCGGGAGTTCACTGGTCTGGGCA
ACTGTATCACCAAGATCTTCAAGTCTGATGGCCTGAGGGGCCTCTACCAGGGTTTCAACGTCTCGGTCCAGGTCCAGGGC
ATCATTATCTACAGAGCTGCCTACTTTGGAGTCTATGATACGGCCAAGGGGATGCTGCCTGACCCCAAGAATGTGCACAT
TATCGTGAGCTGGATGATCGCCCAGACTGTGACAGCGGTCGCGGGGCTCGTGTCCTACCCCTTTGACACTGCCCGCCGTA
GGATGATGATGCAGTCTGGCCAGAAAGGGGCTGATATCATGTACACTGGGACAGTGGACTGCTGGAGGAAGATTGCAAAA
GATGAA

Alignment

ORF - retro_btau_1592 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.93 %
• Parental protein coverage: 80.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSFWRGNLANVIRYFPTQALNFAFKDKY
          V.PIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSFWRGNLANVIRYFPTQALNFAFKDKY
Retrocopy VTPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSFWRGNLANVIRYFPTQALNFAFKDKY

Parental  KQIFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGKGAAQREFTGLGNCITKIF
          KQIFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGKGAAQREFTGLGNCITKIF
Retrocopy KQIFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGKGAAQREFTGLGNCITKIF

Parental  KSDGLRGLYQGFNVSVQ--GIIIYRAAYFGVYDTAKGMLPDPKNVHIIVSWMIAQTVTAVAGLVSYPFDT
          KSDGLRGLYQGFNVSVQ..GIIIYRAAYFGVYDTAKGMLPDPKNVHIIVSWMIAQTVTAVAGLVSYPFDT
Retrocopy KSDGLRGLYQGFNVSVQVQGIIIYRAAYFGVYDTAKGMLPDPKNVHIIVSWMIAQTVTAVAGLVSYPFDT

Parental  VRRRMMMQSGRKGADIMYTGTVDCWRKIAKDE
          .RRRMMMQSG.KGADIMYTGTVDCWRKIAKDE
Retrocopy ARRRMMMQSGQKGADIMYTGTVDCWRKIAKDE

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
ERP005899_liver	0.07 RPM	78.22 RPM
ERP005899_muscle	0.05 RPM	23.70 RPM
SRP017611_brain	0.14 RPM	131.60 RPM
SRP017611_kidney	0.18 RPM	242.54 RPM
SRP017611_liver	0.08 RPM	52.25 RPM
SRP030211_testis	0.04 RPM	33.72 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1592 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1592 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1592 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013208	1 retrocopy	retro_btau_1592 ,
Choloepus hoffmanni	ENSCHOG00000010542	3 retrocopies	retro_chof_1117, retro_chof_1777, retro_chof_807,
Dasypus novemcinctus	ENSDNOG00000007258	3 retrocopies	retro_dnov_1531, retro_dnov_1800, retro_dnov_390,
Dipodomys ordii	ENSDORG00000013787	1 retrocopy	retro_dord_268,
Erinaceus europaeus	ENSEEUG00000001021	2 retrocopies	retro_eeur_274, retro_eeur_36,
Macropus eugenii	ENSMEUG00000008508	4 retrocopies	retro_meug_222, retro_meug_549, retro_meug_6, retro_meug_921,
Microcebus murinus	ENSMICG00000010865	1 retrocopy	retro_mmur_1356,
Oryctolagus cuniculus	ENSOCUG00000002594	1 retrocopy	retro_ocun_102,
Ochotona princeps	ENSOPRG00000005957	6 retrocopies	retro_opri_1154, retro_opri_146, retro_opri_377, retro_opri_517, retro_opri_543, retro_opri_685,
Pan troglodytes	ENSPTRG00000016646	9 retrocopies	retro_ptro_146, retro_ptro_1588, retro_ptro_2143, retro_ptro_2364, retro_ptro_2388, retro_ptro_2517, retro_ptro_2525, retro_ptro_2819, retro_ptro_2882,
Pteropus vampyrus	ENSPVAG00000015279	1 retrocopy	retro_pvam_892,
Sarcophilus harrisii	ENSSHAG00000000932	1 retrocopy	retro_shar_160,
Tarsius syrichta	ENSTSYG00000004233	1 retrocopy	retro_tsyr_27,