RetrogeneDB ID: retro_btau_1223

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:44448435..44449713(+)
• Located in intron of: ENSBTAG00000004591

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZC3H15
• Ensembl ID: ENSBTAG00000021762
• Aliases: None
• Description: Zinc finger CCCH domain-containing protein 15 [Source:UniProtKB/Swiss-Prot;Acc:Q1RMM1]

Sequence

>retro_btau_1223
GTGCCCCCCAAGAAACAGGCTCAGGCCGGGGGCAGCAAAAAGGCGGAGCAGAAAAAGAAGGAGAAGATTATCGAAGACAA
AACTTTTGGTCTGAAGAATAAGAAAGGAGCAAAGCAACAGAAGTTTATCAAGGCTGTCACTCATCAAGTTAAATTTGGTC
AACAGAATCCACGTCAGGTAGCACAAAGTGAAGCTGAAAAGAAGTTGAAGAAAGATGACAAGAAGAAAGAATTGCAAGAG
CTAAATGAGTTGTTCAAACCTGTAGTTGCTGCTCAAAAAATAAGTAAAGGTGCAGATCCCAAATCCGTAGTATGTGCATT
CTTCAAGCAAGGACAGTGTACTAAAGGAGATAAGTGTAAGTTCTCTCATGACTTAACTCTGGAGAGAAAATGTGAAAAGC
GAAGTGTTTACATTGATGCAAGAGATGAAGAACTTGAGAAAGATACTATGGATAATTGGGATGAGAAAAAACTGGAAGAA
GTTGTGAACAAGAAGCACGGTGAGGCGGAAAAGAAAAAACCGAAAACTCAAATAGTGTGCAAGCATTTCCTTGAAGCTAT
TGAAAACGACAAATACGGCTGGTTTTGGGTGTGTCCTGGAGGGGGTGATATTTGCATGTATCGTCATGCACTGCCTCCTG
GATTTGTCTTGAAAAAAGATAAAAAGAAAGAAGAGAAAGAAGATGAAATTTCATTAGAAGATCTAATTGAAAGAGAGCGT
TCTGCCCTAGGTCCAAATGTTACCAAAATCACTCTAGAATCTTTTCTTGCATGGAAGAGAAGAAAAAGACAAGAAAAGAT
TGATAAACTTGAACAAGATATAGAAAGAAGGAAAGCAGACTTCAAAGCTGGGAAAGCATTAGTGATCAGTGGTCGTGAGG
TGTTTGAATTTCGTCCTGAACTGGTTGACAATGATGATGAGGAAGCAGATGATACCCGTTACACCCAGGGAACAGGTGGT
GATGAGGTTGATGATTCAGTGAGTGTAAATGACATAGATTTAAGCCTGTACATCCCAAGAGATGTAGATGAGACAGGTAT
TACTGTAGCCAGTCTTGAAAGATTCAGCACATATACTTCAGAAAAGGATGAAAACAAATTAAGTGAAGCTTCCGGAGGTA
GGGCTGAAAATGGTGAGAGAAGTGATTTGGAAGAGGACAACGAAGGGGAAGGACAGGAAAATGGAGCCATCGATGCTGTT
CCTGTTGATGAAAATCTGTTTACTGGGGAAGATTTGGATGAACAAGAAGAAGAATTAAACACACTTGATTTAGAAGAA

Alignment

ORF - retro_btau_1223 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK
          .PPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK
Retrocopy VPPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK

Parental  KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCTKGDKCKFSHDLTLERKCEKRSVYIDA
          KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCTKGDKCKFSHDLTLERKCEKRSVYIDA
Retrocopy KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCTKGDKCKFSHDLTLERKCEKRSVYIDA

Parental  RDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENNKYGWFWVCPGGGDICMYRHA
          RDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIEN.KYGWFWVCPGGGDICMYRHA
Retrocopy RDEELEKDTMDNWDEKKLEEVVNKKHGEAEKKKPKTQIVCKHFLEAIENDKYGWFWVCPGGGDICMYRHA

Parental  LPPGFVLKKDKKKEEKEDEISLEDLIERERSALGPNVTKITLESFLAWKKRKRQEKIDKLEQDIERRKAD
          LPPGFV..............SLEDLIERERSALGPNVTKITLESFLAWK.RKRQEKIDKLEQDIERRKAD
Retrocopy LPPGFVXXXXXXXXXXXXXXSLEDLIERERSALGPNVTKITLESFLAWKRRKRQEKIDKLEQDIERRKAD

Parental  FKAGKALVISGREVFEFRPELVDDDDEEADDTRYTQGTGGDEVDDSVSVNDIDLSLYIPRDVDETGITVA
          FKAGKALVISGREVFEFRPELVD.DDEEADDTRYTQGTGGDEVDDSVSVNDIDLSLYIPRDVDETGITVA
Retrocopy FKAGKALVISGREVFEFRPELVDNDDEEADDTRYTQGTGGDEVDDSVSVNDIDLSLYIPRDVDETGITVA

Parental  SLERFSTYTSEKDENKLSEASGGRAENGERSDLEEDNEGEGQENGAIDAVPVDENLFTGEDLDELEEELN
          SLERFSTYTSEKDENKLSEASGGRAENGERSDLEEDNEGEGQENGAIDAVPVDENLFTGEDLDE.EEELN
Retrocopy SLERFSTYTSEKDENKLSEASGGRAENGERSDLEEDNEGEGQENGAIDAVPVDENLFTGEDLDEQEEELN

Parental  TLDLEE
          TLDLEE
Retrocopy TLDLEE

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	30.93 RPM
ERP005899_muscle	0.21 RPM	42.50 RPM
SRP017611_brain	0.18 RPM	29.42 RPM
SRP017611_kidney	0.12 RPM	41.49 RPM
SRP017611_liver	0.08 RPM	24.69 RPM
SRP030211_testis	0.59 RPM	92.83 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1223 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1223 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021762	1 retrocopy	retro_btau_1223 ,
Choloepus hoffmanni	ENSCHOG00000011958	1 retrocopy	retro_chof_2120,
Callithrix jacchus	ENSCJAG00000005931	2 retrocopies	retro_cjac_2883, retro_cjac_3986,
Cavia porcellus	ENSCPOG00000012965	2 retrocopies	retro_cpor_1294, retro_cpor_919,
Dipodomys ordii	ENSDORG00000011664	1 retrocopy	retro_dord_666,
Loxodonta africana	ENSLAFG00000001563	1 retrocopy	retro_lafr_941,
Monodelphis domestica	ENSMODG00000027565	5 retrocopies	retro_mdom_1230, retro_mdom_1321, retro_mdom_1744, retro_mdom_1942, retro_mdom_871,
Oryctolagus cuniculus	ENSOCUG00000011903	1 retrocopy	retro_ocun_886,
Otolemur garnettii	ENSOGAG00000002182	2 retrocopies	retro_ogar_1093, retro_ogar_611,
Ochotona princeps	ENSOPRG00000015790	2 retrocopies	retro_opri_169, retro_opri_609,
Pan troglodytes	ENSPTRG00000012717	1 retrocopy	retro_ptro_348,
Rattus norvegicus	ENSRNOG00000005256	4 retrocopies	retro_rnor_2628, retro_rnor_284, retro_rnor_662, retro_rnor_925,
Sorex araneus	ENSSARG00000012071	1 retrocopy	retro_sara_363,