RetrogeneDB ID: retro_btau_1308

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:16910289..16910756(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP1S2
• Ensembl ID: ENSBTAG00000020420
• Aliases: None
• Description: AP-1 complex subunit sigma-2 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZBS3]

Sequence

>retro_btau_1308
ATGCAGTTTATGTTGCTCTTTAGTCGTCAGGGAAAGCTTCAACTACGGAGGTGATGTGTCCCATTATCAGACAAAGAGAA
GAAAAAGATCACAAGAGAACTTCTTCAAACCGTTTTAGCATGGAAACCTAAAATGTGCAGCTTTCTTGAGTGGCGAGATC
TGAAGATTGTTTACAAAAATATGCCAGTCTGTATTTTTGCTGTGCTATTGAGGATCAGGATAATGAACTAATTACCCTGG
AAATAGTTCATCGTTATGTGGAATTACTTGACAAGTATTTTGGCAGTGTGTGCGAATCTGATACCATTTTTAATTTTGAG
AAGGCTTATTTTGTTTTGGATGAGTTTCTTTTGGGAGGAGAAGTTCAGGAAATACCCAAGAATGTCCTTAAAGCAACTGA
GCAGGCTGATCTGCTGCAGGAGGAAGCTGAAACCCTACATAGTGTTCTTGAAGAAATTGGACTGACA

Alignment

ORF - retro_btau_1308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQFMLLFSRQGKLRLQKWYVPLSDKEKKKITRELVQTVLARKPKMCSFLEWRDLKIVYK-RYASLYFCCA
          MQFMLLFSRQGKL.L....VPLSDKEKKKITREL.QTVLA.KPKMCSFLEWRDLKIVYK..YASLYFCCA
Retrocopy MQFMLLFSRQGKLQLRR*CVPLSDKEKKKITRELLQTVLAWKPKMCSFLEWRDLKIVYK<KYASLYFCCA

Parental  IEDQDNELITLEIIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADL
          IEDQDNELITLEI.HRYVELLDKYFGSVCE.D.IFNFEKAYF.LDEFLLGGEVQE...KNVLKA.EQADL
Retrocopy IEDQDNELITLEIVHRYVELLDKYFGSVCESDTIFNFEKAYFVLDEFLLGGEVQEI-PKNVLKATEQADL

Parental  LQEDAKEAETPRSVLEEIGLT
          LQE...EAET..SVLEEIGLT
Retrocopy LQE---EAETLHSVLEEIGLT

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	0.94 RPM
ERP005899_muscle	0.00 RPM	6.55 RPM
SRP017611_brain	0.00 RPM	11.01 RPM
SRP017611_kidney	0.00 RPM	5.22 RPM
SRP017611_liver	0.00 RPM	0.76 RPM
SRP030211_testis	0.00 RPM	12.01 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1308 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1308 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020420	1 retrocopy	retro_btau_1308 ,
Callithrix jacchus	ENSCJAG00000004393	1 retrocopy	retro_cjac_2312,
Dasypus novemcinctus	ENSDNOG00000013888	1 retrocopy	retro_dnov_1786,
Monodelphis domestica	ENSMODG00000017197	7 retrocopies	retro_mdom_1189, retro_mdom_1329, retro_mdom_1441, retro_mdom_1470, retro_mdom_1616, retro_mdom_1987, retro_mdom_903,
Otolemur garnettii	ENSOGAG00000011342	3 retrocopies	retro_ogar_2038, retro_ogar_265, retro_ogar_3453,
Procavia capensis	ENSPCAG00000000733	1 retrocopy	retro_pcap_386,
Pteropus vampyrus	ENSPVAG00000010218	1 retrocopy	retro_pvam_783,
Sorex araneus	ENSSARG00000000117	1 retrocopy	retro_sara_575,
Sarcophilus harrisii	ENSSHAG00000013119	2 retrocopies	retro_shar_651, retro_shar_690,
Sus scrofa	ENSSSCG00000012142	1 retrocopy	retro_sscr_998,
Ictidomys tridecemlineatus	ENSSTOG00000008517	1 retrocopy	retro_itri_131,
Tupaia belangeri	ENSTBEG00000008834	2 retrocopies	retro_tbel_2173, retro_tbel_4575,
Tarsius syrichta	ENSTSYG00000005290	2 retrocopies	retro_tsyr_1953, retro_tsyr_854,
Vicugna pacos	ENSVPAG00000007642	1 retrocopy	retro_vpac_596,