RetrogeneDB ID: retro_btau_727

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:51078104..51078553(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC59
• Ensembl ID: ENSBTAG00000036282
• Aliases: None
• Description: Thyroid transcription factor 1-associated protein 26 [Source:UniProtKB/Swiss-Prot;Acc:A5PJN1]

Sequence

>retro_btau_727
CACCCTGATCACCGGAACCATCTCTACTTAGCTGGAGAGGAAAGACTCAGCAAGCAGCTGAGAAAAGCTGACCAATCCTG
GTTAGAACAAGGTGAGCAGTCTTTGCCAGAAAACCAGGGTACCCCTGACCTTGCTTTGTCTGAAGGACACTGTAGCACTG
AACGGCTTCTGCCAGAAGGGCACTGCAGCACGAGAATATACTCTATGGAACATTCCAAAGCAAAAGAAAACGTCAAACCA
AAAGGCACAGGCAGAATATGAGCAAGCTACGCGTGCTGTGAAGAAACAAGAATTTGAGAGGCAAAAACAAGAGAGAGGAG
AAGCTCCAAGGCTCTACCAACACAAGAAAATGCAAGTGTTCAAGATGCGGAGCCAAAAGACTCTCAAAATGGCAAGCCAA
ATACGGATTTACAAATGGAGTGTTTTCTAAGAAAATACTGGAAAAGAAT

Alignment

ORF - retro_btau_727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.26 %
• Parental protein coverage: 63.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YPDHLKHLYLAEEERLKKQLRKADQPLSEEQVDQPLPEDQGSSDQALSEERCSIEQPQPAEPCSIRINSI
          .PDH..HLYLA.EERL.KQLRKADQ...E.Q..Q.LPE.QG..D.ALSE..CS.E...P...CS.RI.S.
Retrocopy HPDHRNHLYLAGEERLSKQLRKADQSWLE-QGEQSLPENQGTPDLALSEGHCSTERLLPEGHCSTRIYSM

Parental  -NIPKKNKKKTSNQKAQEEYEQIQAKRAAKKQEFERRKQEREEAQRLYKKKKMEVFKILSKKT-KKGQPN
          .NIPK...KKTSNQKAQ.EYEQ..A.RA.KKQEFER.KQER.EA.RLY..KKM.VFK..S.KT..K.Q..
Retrocopy >NIPKQ--KKTSNQKAQAEYEQ--ATRAVKKQEFERQKQERGEAPRLYQHKKMQVFKMRSQKT>SKWQAK

Parental  LNLQMEYLLKKIQENN
          .........KKI.E.N
Retrocopy YGFTNGVFSKKILEKN

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	0.00 RPM	24.95 RPM
ERP005899_muscle	0.00 RPM	11.19 RPM
SRP017611_brain	0.00 RPM	16.08 RPM
SRP017611_kidney	0.00 RPM	16.00 RPM
SRP017611_liver	0.00 RPM	10.87 RPM
SRP030211_testis	0.00 RPM	109.83 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_727 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_727 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016875	1 retrocopy	retro_amel_954,
Bos taurus	ENSBTAG00000036282	4 retrocopies	retro_btau_725, retro_btau_726, retro_btau_727 , retro_btau_728,
Choloepus hoffmanni	ENSCHOG00000007788	1 retrocopy	retro_chof_1648,
Dasypus novemcinctus	ENSDNOG00000011546	1 retrocopy	retro_dnov_1033,
Dipodomys ordii	ENSDORG00000003005	1 retrocopy	retro_dord_485,
Echinops telfairi	ENSETEG00000000256	2 retrocopies	retro_etel_1338, retro_etel_1789,
Gorilla gorilla	ENSGGOG00000025296	2 retrocopies	retro_ggor_1386, retro_ggor_99,
Microcebus murinus	ENSMICG00000000967	4 retrocopies	retro_mmur_1456, retro_mmur_354, retro_mmur_689, retro_mmur_909,
Oryctolagus cuniculus	ENSOCUG00000017824	2 retrocopies	retro_ocun_1782, retro_ocun_498,
Otolemur garnettii	ENSOGAG00000004383	1 retrocopy	retro_ogar_2065,
Pan troglodytes	ENSPTRG00000005266	1 retrocopy	retro_ptro_1270,
Tupaia belangeri	ENSTBEG00000008887	7 retrocopies	retro_tbel_1515, retro_tbel_2047, retro_tbel_2126, retro_tbel_302, retro_tbel_3391, retro_tbel_3721, retro_tbel_972,